http://fgf.genomics.org.cn/service/index.jsp FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations). FGF http://david.abcc.ncifcrf.gov/home.jsp The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. DAVID Bioinformatics Resources http://fralanyzer.cse.buffalo.edu/ FRalanyzer (Fold Recognition alignment analyzer) takes as input a sequence-structure alignment, automatically searches annotated databases, and highlights the functionally important positions that are identical in the alignment. FRalanyzer http://conseq.bioinfo.tau.ac.il/ ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq http://tagc.univ-mrs.fr/erpin/ ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs. ERPIN http://mouseSNP.roche.com Free access to a database developed by Roche. The Mouse SNP Database http://cg1.iis.sinica.edu.tw/~mybs/index.php MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases. MYBS http://arep.med.harvard.edu/mrnadata/mrnasoft.html Scans for Nucleic Acid Conserved Elements scans DNA sequence for over-represented oligomers to find elements which match a DNA motif; free for non-commercial use with license agreement. ScanACE http://projects.villa-bosch.de/dbase/molsurfer/ Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/ RNA interfaces. MolSurfer http://www.bcgsc.ca/bioinfo/software/discoveryspace/ DiscoverySpace is a tool for gene expression analyses and biological discovery. DiscoverySpace http://www.blueprint.org/index.html Bioinformatics research program affiliated with the Samuel Lunenfeld Research Institute at Mount Sinai Hospital at the University of Toronto. Blueprint is actively researching protein folding and molecular structure, location, dynamics, sequence, interaction and evolution as they relate to systems biology in an effort towards simulating a living cell The Blueprint Initiative http://www.imtech.res.in/raghava/gpcrpred/ GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user- supplied query sequence. GPCRpred http://www.mlst.net/ MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes. MLST http://www.megasoftware.net/ MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments. MEGA The European Bioinformatics Institute (EBI) The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. The EBI web page is a portal to various public access databases and tools for information retrieval, analysis, and data submission provided by the EBI. The services include access to sequence, literature, microarray, and structure databases, and to tools such as BLAST, ClustalW, DALI, and InterProScan for sequence, structural and functional analysis. Various databases and software tools are also downloadable via FTP. http://www.ebi.ac.uk/ http://genome.ucsc.edu/cgi-bin/hgGateway? org=Fruitfly&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the fruitfly genome at any scale, together with dozens of aligned annotation tracks. UCSC Fruitfly Genome Browser Gateway http://olduvai.sourceforge.net/ TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences. TreeJuxtaposer http://visant.bu.edu/ VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java- based, and can be run as a java applet, as a java web application, or downloaded and run locally. VisANT http://weblogo.berkeley.edu/ WebLogo allows one to create graphical representations (sequence logos) of multiple sequence alignments. This can be done from the website and the source code for WebLogo is also available for download. WebLogo http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/ PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). PathExpress http://www.pmap.csupomona.edu/MINER/ MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family). MINER http://www.protarget.cs.huji.ac.il/index.php ProTarget offers a method for the prediction of novel structural superfamilies by assessing the relationship of input protein sequences to previously solved 3D structures. ProTarget http://scop.mrc-lmb.cam.ac.uk/scop/ Structural Classification of Proteins - database created by a combination of manual inspection and automated methods. SCOP http://www.bioinformatics.ubc.ca/pegasys/ Pegasys is a a flexible, modular and customizable software system that coordinates the execution of multiple biological sequence analysis tools and facilitates the integration of their output. The software allows users to create analysis workflows using a graphical user interface. Adaptors are included for various software tools. Pegasys: workflow management for bioinformatics http://www.cbs.dtu.dk/services/FeatureMap3D/ FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB. FeatureMap3D Sequence_Feature_Detection http://prdos.hgc.jp/cgi-bin/top.cgi PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence. PrDOS http://rvista.dcode.org/ Server which detects transcription factor binding sites (TFBS) through combining TFBS prediction, sequence comparison and cluster analysis. rVISTA http://us.expasy.org/alinks.html Extensive list of links to biology resources; compiled by Amos Bairoch of SWISS-PROT. Amos WWW links page Alignment_Editing_and_Visualization http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ a system of databases documenting the influence of mutations in regulatory gene regions rSNP_Guide http://www.cbr.nrc.ca/ Provides biologists across Canada access to bioinformatics applications, large-volume data storage, basic training, and help desk support; available to National Research Council scientists, academic/not-for-profit users associated with a university, hospital, or government department. Canadian Bioinformatics Resource http://vega.sanger.ac.uk In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence. Vega Annotation Browser http://binf1.chem.mq.edu.au:8080/est_pipeline/wrapper_files/ login_page_main ESTExplorer is an automated suite of programs to pre- process, assemble and functionally annotate ESTs at both DNA and protein level. ESTExplorer http://www.hubmed.org/ HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature. HubMed https://fungalgenome.concordia.ca/tools/TargetIdentifier.html TargetIdentifier is designed for identifying full-length EST cDNAs and functionally annotating EST cDNAs. TargetIdentifier http://www.ebi.ac.uk/Wise2/ The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. Wise2 http://www.yourgenome.org/ A resource site from the Wellcome Trust Sanger Institute with information on genomes and the social implications of genomic science. It is organized into three sections based on the background knowledge of the reader. Yourgenome.org http://www.ncbi.nlm.nih.gov/BankIt/ Web-based submission of one or a few sequences to GenBank. BankIt http://973-proteinweb.ustc.edu.cn/gps/gps_web/predict.php Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences. GPS http://www.ncbi.nlm.nih.gov/books/bv.fcgi? call=bv.View..ShowTOC&rid=toolkit.TOC&depth=2 The NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications. NCBI C++ toolkit http://www.gsc.riken.go.jp/e/FANTOM/ Functional annotations for RIKEN full-length cDNA clones. FANTOM - Functional Annotation of Mouse http://www.cprogramming.com/ Cprogramming.com is a web site designed to help you learn C or C++ and provide you with C and C++ programming resources. Cprogramming.com http://www.bioconductor.org/ Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data. Bioconductor http://andromeda.gsf.de/litminer LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, compounds, diseases and phenotypes, and tissues and organs. LitMiner http://mendel.imp.univie.ac.at/PhyloDome/ PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains. PhyloDome Multiple_Sequence_Alignments http://www.cs.ualberta.ca/~bioinfo/PA/Sub/ PA-SUB (Proteome Analyst Specialized Subcellular Localization Server) can be used to predict the subcellular localization of proteins using established machine learning techniques. PA-SUB http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist. Build your own arrayer http://bioverse.compbio.washington.edu/ Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information. Bioverse http://babelomics.bioinfo.cipf.es/ Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Babelomics http://bioinfo3d.cs.tau.ac.il/ARTS/ Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures. ARTS http://www.cbs.dtu.dk/services/OligoWiz2/ OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript. OligoWiz http://protevo.eb.tuebingen.mpg.de/repper REPPER (REPeats and their PERiodicities) is a tool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats. REPPER http://genome-www5.stanford.edu/ SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Stanford Microarray Database (SMD) http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/ Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids. CRASP http://cic.cs.wustl.edu/wordspy/ WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription factor binding motifs. WordSpy http://genome.ewha.ac.kr/ASePCR/ ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs. ASePCR Fly http://genome.ucsd.edu/VAMPIRE/ VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data. VAMPIRE http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Influenza Virus Resources http://sourceforge.net/projects/orb-cct CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases. CCT http://genome.lbl.gov/vista/index.shtml VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. VISTA http://bioinformatics.ustc.edu.cn/LOCSVMPSI/LOCSVMPSI.php LOCSVMpsi is a tool for prediction of eukaryotic protein subcellular localization based on support vector machines (SVM) and PSI-BLAST. LOCSVMpsi http://www.genomenewsnetwork.org/ Bi-weekly online news magazine, covering genomics, proteomics, and related news in biomedical, microbial, and agricultural research; publication of The Institute for Genomic Research (TIGR). Genome News Network http://proteindbs.rnet.missouri.edu/ ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS http://www.ncbi.nlm.nih.gov/SAGE/index.cgi SAGE tag to gene mapping by NCBI. SAGEmap http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/ Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites. SITECON http://pupasuite.bioinfo.cipf.es PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView. PupaSuite http://mendel.imp.univie.ac.at/mendeljsp/index.jsp The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences. The Mendel Site http://sirna.cgb.ki.se/ This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs). siRNAdb http://snpnavigator.net/ SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented. SNP@Domain http://dunbrack.fccc.edu/pisces/ PISCES (Protein Sequence Culling Server) allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity. PISCES http://snpanalyzer.utmem.edu/ nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated. nsSNPAnalyzer http://pdb2pqr.sourceforge.net/ Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures. PDB2PQR Server http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM Online Mendelian Inheritance in Man; catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed. OMIM http://ibivu.cs.vu.nl/programs/scoobywww/ Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. Scooby-domain http://cubic.bioc.columbia.edu/db/LOC3d/ LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences. Loc3D http://microarrays.unife.it/ Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis. GOAL http://prometheus.brc.mcw.edu/promost/ ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images. ProMoST http://www.jenner.ac.uk/BPROMPT/ Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence. BPROMPT http://www.onjava.com/ O'Reilly Network's source for Java news and information. ONJava.com http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts. RCI http://gcua.schoedl.de Graphical representation of codon bias GCUA: Graphical Codon Usage Analyser http://www.bioinformatics.leeds.ac.uk/betaBarrel/ TMB-Hunt (Transmembrane Barrel - Hunt) classifies protein sequences as transmembrane B-barrel (TMB) or non-TMB based on amino acid composition. TMB-Hunt http://ps2.life.nctu.edu.tw (PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T- Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER. (PS)2 Protein Structure Prediction Server http://depts.washington.edu/~yeastrc/index.html Provides expertise and access through collaboration to mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction; very good info on each of the techniques. Yeast Resource Center http://searchlauncher.bcm.tmc.edu/seq-util/readseq.html Sequence format conversion; includes GenBank, EMBL, GCG, FASTA, ASN.1, Phylip and others. ReadSeq http://schubert.bio.uniroma1.it/SCR_FIND/ SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments. SCR_FIND http://genes.mit.edu/burgelab/rescue-ese/ Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes. Rescue-ESE http://svc.molgen.mpg.de/ SVC (Structured Visualization of Evolutionary Conserved Sequences) is a tool that can search for pairs of orthologous genes, align the protein coding sequences, and visualize the evolutionary sequence conservation mapped back onto the gene structure scaffold. SVC IBM Genome Annotation Page IBM's Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (archae, bacteria, eurkaryotes, and viruses). You can query these annotations at the sequence level as well as search/compare across genomes. http://cbcsrv.watson.ibm.com/Annotations/home.html http://www.nature.com/omics/index.html A comprehensive web resource devoted to genomics. Sections include papers, news, the human-genome, and post-genomics. Nature's Genome Gateway Biochemical_Features http://www.statistics.com/ Online statistics courses. Also contains links to statistics software and on-line textbooks. Statistics.com http://oxytricha.princeton.edu/BlastO/index.html BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences. BLASTO http://pbil.univ-lyon1.fr/sim4.php Align cDNA with genomic DNA, allowing for introns and small number of sequencing errors. SIM4 http://research.i2r.a-star.edu.sg/DRAGON/TFAM_v2/index.html Dragon TF Association Miner (DTFAM) is text-mining tool which takes Pubmed abstracts/summaries as input and reports potential associations between transcription factors and diseases/GO ontologies. The user can also provide a PubMed query directly to DTFAM and its output will be analysed when the search has completed. There is a limit of 5000 abstracts per session. DTFAM http://us.expasy.org/enzyme/ Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only. ENZYME - Enzyme nomenclature database http://fastsnp.ibms.sinica.edu.tw/pages/ input_CandidateGeneSearch.jsp Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects. FastSNP http://www.ebi.ac.uk/InterProScan/ InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence. InterProScan http://www.ncbi.nlm.nih.gov/genomes/static/links.html Genome centers and databases listed by organism. Genome Centres and Databases Other_Resources Sequence_Polymorphisms http://gemdock.life.nctu.edu.tw/fastSCOP/ fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D- BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries. fastSCOP http://www.ch.embnet.org/software/TMPRED_form.html Prediction of transmembrane regions and their orientation. TMpred http://schubert.bio.uniroma1.it/CHC_FIND/index.html CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided. CHC_FIND http://pre-s.protein.osaka-u.ac.jp/~prebi/ Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area. PreBI http://www.bioinformatics.ca/course_listings.php A list of bioinformatics courses available at Canadian post-secondary institutions. Canadian Bioinformatics Course Listings http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.html Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures. Motif3D http://origin.bic.nus.edu.sg/mgalign/mgalignit.html mRNA to Genome Alignments (MgAlignIt) aligns mRNA/EST to genome sequences and visualizes the alignment to provides intron/exon structure information. MGAlignIt http://phylogenomics.berkeley.edu/ The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification. Berkeley Phylogenomics Group http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns. PatMatch http://www.nhgri.nih.gov/DIR/Microarray/main.html Protocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available). NHGRI Micorarray Project http://159.149.109.16/modtools/ Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences. MoD Tools http://www.bioinformatics.ca/people/people_canada.php Principal investigators and group leaders from academia, government labs, and industry with an interest in development of bioinformatics resources in Canada. Canada Bioinformatics People http://www.plos.org/ The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource. Public Library of Science http://iris.physics.iisc.ernet.in/bsdd/ BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization. BSDD Plants http://dilimot.embl.de/ Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins. DILIMOT http://www.blueprint.org/seqhound/api_help/ seqhound_help_guides.html SeqHound is a bioinformatics application programming platform that provides access to biological sequence, structure and functional annotation data. An application programming interface (API) is available to programmers using C, C++, Java and PERL. Seqhound API http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/ pdbsitescan.html PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites. PDBSiteScan http://www.ebi.ac.uk/embl/Submission/webin.html WEBIN is the internet tool for the submission of nucleotide sequences to the EMBL database. It is a service offered by the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory. WEBIN Structure_Prediction__Visualization__and_Design http://www.ch.embnet.org/ Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics. Swiss EMBnet http://datalab.njit.edu/biodata/rna/RSmatch/server.htm RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences. RADAR http://www.informatics.jax.org/ Integrated access to data on mouse genetics, genomics and biology; Jackson Labs. Mouse Genome Informatics http://math-cs.cns.uni.edu/~okane/cgi-bin/newpres/marbl/ MARBL is an open-source package for indexing the text components of GenBank records and the NLM article abstracts associated with them. A few demonstrations of the package are also available at this website. MARBL http://bioware.ucd.ie/~slimdisc/ SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub- cellular location or a common interaction partner. SLiMDisc http://genome-www.stanford.edu/Saccharomyces/VL-yeast.html Links to yeast resources. Virtual Library--Yeast http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis. ACT http://psfs.cbrc.jp/fold-rate/ FOLD-RATE predicts the folding rates of proteins from their amino acid sequences. FOLD-RATE http://distill.ucd.ie/spritz/ Spritz is a tool for the prediction of disordered regions of proteins. Spritz http://www.usm.maine.edu/~rhodes/SPVTut/index.html Excellent hands-on Swiss-PdbViewer/Deep View tutorial; a must-do before attempting to use Swiss-PdbViewer. Molecular Modeling for Beginners http://www.open-bio.org/ The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. Open Bioinformatics Foundation http://www.cbs.dtu.dk/services/NetOGlyc/ Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins. NetOGlyc Prediction Server Courses__Programs_and_Workshops http://www.ogic.ca/projects/g2d_2/ G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. G2D http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them. Zinc Finger Tools http://ef-site.hgc.jp/eF-seek/index.jsp eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites. eF-seek http://manaslu.aecom.yu.edu/M4T/ M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments. M4T http://rulai.cshl.edu/tools/ESE/ ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing. ESEfinder http://blocks.fhcrc.org/sift/SIFT.html Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function. SIFT Pairwise_Sequence_Alignments Presentation_and_Format Annotations http://pfp.technion.ac.il/ PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces. PFP http://biunit.aist-nara.ac.jp/Matras/ MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures. MATRAS http://polydoms.cchmc.org/polydoms/ PolyDoms is a database that maps human coding SNPs onto protein domains in an effort prioritize candidate mutations and polymorphisms. PolyDoms http://mbcf.dfci.harvard.edu/cmsmbr/ Compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry and Biomolecular Modeling. CMS Molecular Biology Resource http://www.genetics.wustl.edu/eddy/tRNAscan-SE/ tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Eddy Lab at WashU) tRNAscan-SE http://www.wdcm.org/AHMII/ahmii.html Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines. AHMII http://oralhistory.cshl.edu/mainMovie.html A collection of oral histories through the eyes of more than fifty scientists who have worked at and visited Cold Spring Harbor Laboratory. Provides a great perspective on the early years of molecular biology and visions of the future from leading scientists. CSHL Oral History Collection http://www.genome.ad.jp/ Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web- based tools for sequence analysis (ie. Blast, Motif, Clustal W) GenomeNet http://www.genomesonline.org/ Up-to-date list of complete and ongoing genome projects. GOLD: Genomes Online Database http://stubb.rockefeller.edu/ Stubb uses a probabilistic model and a maximum likelihood approach to detect clusters of transcription factor binding sites (TFBS) in genomic sequences (limit of 100 Kb). It can also use related genomes to improve module prediction accuracy. Stubb http://biodev.hgen.pitt.edu/Footer/ Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences. Footer http://bioserv.rpbs.jussieu.fr/Help/FAFDrugs.html Free ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process. FAF-Drugs http://bioinf.cs.ucl.ac.uk/psipred/ An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction. PSIPRED http://kobas.cbi.pku.edu.cn KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occuring (or significantly enriched) pathways among the queried sequences compared against a background distribution. KOBAS http://pdbfun.uniroma2.it/ pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type. pdbFun http://cubic.bioc.columbia.edu/services/proftmb/ PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes. PROFtmb http://linux.com This site has great tutorials and links to other linux sites, supported by the OSDN. Linux.com http://www.mcb.mcgill.ca/ The Centre for Bioinformatics at McGill is committed to developing the area as a focus of academic research excellence. McGill Centre for Bioinformatics http://cluster-1.mpi-cbg.de/Deqor/deqor.html Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity. DEQOR http://bioinformatics.org/sewer/ Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools. SeWeR http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=PubMed Entrez-searchable database of biomedical literature citations with links to molecular resources at the NCBI. PubMed http://caps.ncbs.res.in/imot/iMOTserver.html iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3- dimensional structures. iMOT http://mouse.ensembl.org/ Analysis of finished and draft mouse genomic clone sequences. Ensembl Mouse Genome Browser http://genometrafac.cchmc.org/genome-trafac/index.jsp GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs. GenomeTraFaC http://210.212.212.6/icr/index.html Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes. iCR http://db.psort.org/ PSORTdb is a database of proteins of experimentally known (ePSORTdb) and computationally predicted (cPSORTdb) subcellular localization. PSORTdb http://hodgkin.mbu.iisc.ernet.in/~prodoc/ PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information. PRODOC http://rocky.bms.umist.ac.uk/SiteSeer/ SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes. SiteSeer http://eureka.ims.u-tokyo.ac.jp/asian/ ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling. ASIAN http://bindr.gdcb.iastate.edu/RNABindR/ RNABindR is a server for analyzing and predicting RNA binding sites in proteins. RNABindR http://www-lbit.iro.umontreal.ca/RNA_Links/RNA.shtml An exhaustive list of RNA links; from the experts in the Major lab. RNA Informatics Links http://www.sanger.ac.uk/Software/Pfam/ Collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam http://www.the-scientist.com/ News journal for the life scientist. The Scientist http://www.ebi.ac.uk/parasites/parasite-genome.html Parasite genome databases and genome research resources. Parasite-Genome http://www.perl.org/ Perl Mongers - The Perl advocacy people. Perl Mongers http://cubic.bioc.columbia.edu/services/DSSPcont/ DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations. DSSPcont http://atgc.lirmm.fr/mam/ This is the web version of the Multiple alignment Manipulator (MaM), which takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/ information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions. WebMAM http://www.bcgsc.bc.ca/ Deploy resources and technology of a high-throughput genome mapping and DNA sequencing lab to decrypt the genetic code, specifically to advance cancer research, diagnosis, and treatment. Genome Sciences Centre, Vancouver http://blocks.fhcrc.org/codehop.html COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences. CODEHOP http://eshadow.dcode.org/ A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements. eShadow https://carmaweb.genome.tugraz.at/carma/ Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor. CARMAweb http://glycan.genome.ad.jp/ The KEGG Carbohydrate Matcher (KCaM) takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm. KCaM http://www.genome.wisc.edu/ U.Washington E. coli genome project site maintains and updates the annotated sequence of the E. coli K12 genome; also has resources and tools for functional characterization of E. coli genes E. coli Genome Project http://www.tree-puzzle.de/#puzzleboot Puzzleboot is a UNIX shell script facilitating bootstrap analysis using TREE-PUZZLE and PHYLIP. It enhances TREE-PUZZLE by allowing one to analyse multiple datasets, and can be used for both protein and DNA distance bootstrap analysis. Puzzleboot http://monster.northwestern.edu/ MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site. MONSTER http://trantor.bioc.columbia.edu/SMS/ STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them. STING Millenium http://www.mekentosj.com/programs/index.html Freely available programs that run on the MacOSX platform. 4Peaks is a DNA sequence editor and visualization program able to read and write common trace file formats. iRNAi assists in the design of error-free oligos. EnzymeX is a tool to help determine which restriction enzymes to use and includes information for over 580 enzymes. LabAssistant is a task/time management system to help organize your experiments. Software for MacOSX at Mek&Tosj.com http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/ software/index.html GraBCas is a tool for predicting granzyme B and caspase cleavage sites. GraBCas http://toolkit.tuebingen.mpg.de Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. MPI Toolkit http://www.tldp.org/ The Linux Documentation Project is a repository of Linux documentation including documents about individual software, HOWTO documents, FAQs, and more. Linux Documentation Project http://www.cs.nuim.ie/distributed/multiphyl.php MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines. MultiPhyl http://zpicture.dcode.org/ zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista. zPicture and multi-zPicture http://bio.cs.washington.edu/software.html FootPrinter is a program for phylogenetic footprinting that identifies regions of DNA that are well conserved across a set of orthologous sequences in order to infer phylogenetic relationships. FootPrinter http://rsat.ccb.sickkids.ca/ Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. RSAT http://www.rostlab.org/services/LOCtarget/ LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks. LOCtarget http://www.daimi.au.dk/~compbio/pfold The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure. Pfold http://www.reactome.org/ Reactome is a database of human biological pathways and processes ranging from basic processes of metabolism to complex regulatory pathways. The data is curated by biologists and subsequently peer-reviewed for accuracy and consistency. Cross- references with UniProt, PubMed, Ensembl, Gene Ontology and LocusLink are also provided. Reactome supersedes The Genome Knowledgebase project. Reactome - a knowledgebase of biological processes http://bioknoppix.hpcf.upr.edu/ BIOKNOPPIX is a live distribution of the Linux operating system that can be run from a CD drive (see also KNOPPIX). BIOKNOPPIX is loaded with bioinformatics applications. BIOKNOPPIX http://redpoll.pharmacy.ualberta.ca/drugbank/index.html DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14,000 protein or drug target sequences are linked to these drug entries. DrugBank http://dicsoft2.physics.iisc.ernet.in/sem/ Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary. SEM http://www.ncbi.nlm.nih.gov/Education/index.html What is bioinformatics? Why use bioinformatics? excellent tutorials on BLAST and the Entrez search and retrieval system. NCBI Education http://oxytricha.princeton.edu/SWAKK/ Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure. SWAKK http://www.tigr.org/tdb/humgen/bac_end_search/ bac_end_intro.html TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; these sequences provide highly specific markers. Human BAC Ends http://salilab.org/our_resources.shtml This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF). Andrej Sali Lab http://biopython.org/ The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. BioPython http://www.genepath.org/genepath2 GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data. GenePath http://advice.i2r.a-star.edu.sg/ Automated Detection and Validation of Interaction by Co- Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions. ADVICE http://sts.bioengr.uic.edu/castp/ Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins. CASTp http://zlab.bu.edu/CARRIE-web Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated. CARRIE Sequence_Retrieval_and_Submission http://www.bioinformatics.nl/tools/treedom TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment. TreeDomViewer http://dna.bio.puc.cl/tm.html dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available; list of other melting temperature calculation servers also provided. dnaMATE http://pbil.univ-lyon1.fr/software/njplot.html NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Available for several platforms including Windows, MacOS, Linux and Solaris. NJplot http://www.bioinfo.rpi.edu/applications/mfold/old/rna/ Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS. Mfold Sequence_Retrieval http://research.i2r.a-star.edu.sg/CysView/ CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns. CysView http://source.stanford.edu Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat. SOURCE http://griffin.cbrc.jp/ GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity. GRIFFIN http://www.knoppix.net/ Knoppix is a GNU/Linux distribution that boots and runs completely from cd. It includes recent linux software and desktop environments, with programs such as OpenOffice.org, Abiword, The Gimp, Konqueror, Mozilla, and hundreds of other quality open source programs. Knoppix http://www.t-profiler.org/ T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes. T-profiler Other_Alignment_Tools http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/ WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated. WebProAnalyst http://genomeold.wustl.edu/groups/informatics/software/polybayes/ UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use. PolyBayes http://foldx.embl.de/ FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein. FoldX http://www.bioinformatics.ca/program_listings.php A list of bioinformatics programs available at Canadian post-secondary institutions. Canadian Bioinformatics Programs http://www.distrowatch.com/ This site is an attempt to provide a basic feature list and a package comparison table of major, minor and regional Linux distributions. It is updated daily with news from the Linux distribution world. Linux DistroWatch http://polymerase.ucd.ie/cgi-bin/pKa_Design/server_start.cgi pKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change. pKD http://www.ebgm.jussieu.fr/~gelly/index.html Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures. Protein Peeling http://bips.u-strasbg.fr/PromAn/ PromAn is an integrated promoter analysis platform that takes a genomic sequence of interest and considers information on orthologous genomic sequence(s), user submitted patterns, and public databases to predict transcription start sites (TSS), transcription factor binding sites (TFBS), and to carry out phylogenetic footprinting. PromAn http://www.ch.embnet.org/software/COILS_form.html Prediction of coiled coil regions. COILS http://mirna.imbb.forth.gr/microinspector/ MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites. MicroInspector http://www.proweb.org/parsesnp/ Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes. PARSESNP http://rocaplab.ocean.washington.edu/tools/repk REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups. REPK http://bioinfo.ernet.in/cep.htm CEP (Conformational Epitope Prediction) is a server for the prediction of probable antibody binding sites of protein antigens. CEP http://protemot.csie.ntu.edu.tw/ The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB. Protemot http://bioinformoodics.jhmi.edu/quickSNP.pl QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module. QuickSNP http://thegpm.org/ The Global Proteome Machine (GPM) project facilitates the analysis of proteomes for researchers using tandem mass spectrometry. The aims of the project include providing a common validation and testing platform for results, making the results more portable, and improving the quality of the analysis. The GPM uses the X! TANDEM Spectrum Modeler to match peptide sequences to tandem mass spectra. Both the GPM interface and X! TANDEM are open-source. The Global Proteome Machine http://firedb.bioinfo.cnio.es/Php/FireStar.php Firestar predicts functionally important residues, such as ligand binding sites, using structural templates and alignment reliability. firestar http://jafa.burnham.org/ Joined Assembly of Function Annotations (JAFA) queries multiple functional annotation servers including GOblet, GOfigure, GOtcha, and InterProScan to return the gene ontology (GO) terms that are associated with your protein sequence highlighting where the results from different servers agree. JAFA http://phospho.elm.eu.org/ Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data formerly found in PhosphoBase. Phospho.ELM http://www.lipidmaps.org/tools/index.html LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data. LIPID MAPS http://pbil.univ-lyon1.fr/ Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses. PBIL http://us.expasy.org/ch2d/ This is a 2D gel electrophoresis database containing data for proteins identified on SDS-PAGE or 2D-PAGE reference maps. SWISS-2DPAGE http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p- match.cgi P-Match is a transcription factor binding site identification tool that increases its accuracy by combining weight matrix and pattern matching approaches. Registration at the site is free and is required to use P-Match. P-Match http://www.cisreg.ca:8080/ulysses/ Ulysses is a system to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated through the framework of a large database. The system unites homology mapping through HomoloGene and the integrated database Atlas. Ulysses http://cbi.labri.fr/outils/alias/ A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand- alone tool. AliasServer http://structure.pitt.edu/servers/fastcontact/ FastContact is a free energy scoring tool for protein- protein complex structures. FastContact http://modi.uos.ac.kr/modi/ Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide. MODi http://blast.wustl.edu/maskeraid/ MaskerAid is an enhancement to RepeatMasker which can effect about a 30-fold increase in the speed of RepeatMasker while maintaining sensitivity. MaskerAid http://gel.ahabs.wisc.edu/mauve/documentation.php Mauve is a stand-alone software tool for constructing multiple genome alignments. Mauve http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/ match.cgi? Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match. Match http://bayesweb.wadsworth.org/gibbs/gibbs.html Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS). Gibbs Motif Sampler http://cbr-rbc.nrc-cnrc.gc.ca/services/genematcher_e.php The GeneMatcher is a computer specialized for executing calculation intensive methods in bioinformatics. It has 6912 specialized data processors which allow otherwise computationally prohibitive searches to be run quickly in parallel. GeneMatcher http://fasta.bioch.virginia.edu/ Sequence retrieval and comparison tools. FASTA Programs http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I- Mutant2.0.cgi I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures. I-Mutant2.0 Search_Tools https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures. NQ-Flipper http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values. ArrayPipe http://www.cmdr.ubc.ca/bobh/PAAP.html Pseudomonas aeruginosa community annotation project (PseudoCAP); information and tools for genome analysis and annotation of P. aeruginosa. PseudoCAP http://biomechanics.ecs.umass.edu/umms.html UMass Morph Server (UMMS) is a tool for molecular dynamics simulations that can be used for visualizing and predicting motions of macromolecules such as conformational changes in protein structures. UMMS http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html Includes reverse complement, 6-frame translation, RepeatMasker, ReadSeq format conversion. BCM Search Launcher Sequence Utilities http://www.bioinfo.rpi.edu/applications/mfold/ Algorithms, thermodynamics and databases for RNA secondary structure. The Zuker Group http://bioinformatics.ramapo.edu/QGRS/index.php Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene. QGRS Mapper http://biosun1.harvard.edu/complab/chipinfo/ ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine. ChipInfo http://estpass.kobic.re.kr/index.jsp ESTpass is a server for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass http://rana.lbl.gov/EisenSoftware.htm Eisen Lab software for microarry image processing, analysis and visualization; available for download to windows platforms only; free with registration for non-commercial use. ScanAlyze, Cluster, TreeView http://bioinfo.lifl.fr/carnac Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned. CARNAC http://www.athamap.de/ AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana AthaMap http://www.ncbi.nlm.nih.gov/sutils/e-pcr Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis- priming events. Electronic PCR http://bioinformatics.org/textknowledge/acronym.php The acronym database provides free access to medical/ biological acronyms. It has 100,000+ acronyms and the users can also contribute by rating the entries quality. In the backend, it is generated from medline data. Medical Acronym Finder http://www.hmdb.ca/ The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches. HMDB Computer_Related http://compbio.cs.sfu.ca/MAM.htm The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions. MaM http://www.cmbi.ru.nl/GeneSeeker/ GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases. GeneSeeker Open_Access_Resources http://i.moltalk.org iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a structure, search for contacts for a residue, and identify the interface between chains. iMolTalk Sequence_Features http://www.pesolelab.it/ Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary. Web Weeder http://bioserv.rpbs.jussieu.fr/websage/ WebSage is a tool that performs statistical analysis of SAGE data. WebSage http://us.expasy.org/tools/peptide-mass.html Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides. PeptideMass http://webclu.bio.wzw.tum.de/stride/ STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map. STRIDE Small_Molecules http://iscb.org/univ_programs/program_board.php A list of university programs in bioinformatics and computational biology maintained by the ISCB. Degree Programs in Bioinformatics and Computational Biology http://cbio.ca Home of the Ontario community of Computational Biologists Computational Biology Institute of Ontario http://www.genetics.med.ed.ac.uk/prospectr/ Prospectr (PRiOrization by Sequence & Phylogenetic Extent of CandidaTe Regions) can be used to enrich lists of genes found at a suspected disease locus. Given a list of genes, Prospectr will return a ranked list ordered by the likelihood of involvement in disease. Prospectr http://cgap.nci.nih.gov/ Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data. Cancer Genome Anatomy Project http://past.in.tum.de/ Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids. PAST http://www.arabidopsis.org/ Comprehensive resource for the scientific community working with Arabidopsis thaliana. The Arabidopsis Information Resource (TAIR) http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites. JASPAR http://www.medinfopoli.polimi.it/GFINDer/ Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources. GFINDer http://cluster.physics.iisc.ernet.in/3dss/options.html 3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary. 3DSS http://proline.bic.nus.edu.sg/sdpmod/ SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs). SDPMOD http://www.benoslab.pitt.edu/stamp/ STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching. STAMP Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved. YOGY http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ http://bioinformatics.med.ohio-state.edu/ The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict first exon and promoter regions and a software toolkit for developing web-based applications to view genomic data. OSU Bioinformatics and Computational Biology http://www.expasy.org/ Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE. ExPASy Molecular Biology Server http://projects.villa-bosch.de/dbase/ps2/ Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures ProSAT2 http://www.coachorg.com/default.asp?id=367 Canadian Organzation for the Advancement of Computers in Health (COACH) is an organization that promotes understanding of health informatics within the Canadian health system through education, information, networking and communication. COACH http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/PlantGDBgs.cgi GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes. GeneSeqer http://www.dnalc.org/ddnalc/websites/ excellent online genetics activities, including BioServers bioinformatics tools designed for teachers and students, and animations explaining techniques such as PCR. DNA Learning Center, Cold Spring Harbor Laboratory http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea. NAST http://interweaver.i2r.a-star.edu.sg/ InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions. InterWeaver http://www.ncbi.nlm.nih.gov/projects/assembly/ The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive's raw sequence data. NCBI Assembly Archive General http://bioinfo3d.cs.tau.ac.il/ BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions. BioInfo3D http://dove.embl-heidelberg.de/Blast2e/ BLAST a protein sequence then perform automated phylogenetic analysis to detect orthologous sequences. Orthologue Search Service http://genome.cbs.dtu.dk/services/HMMgene/ Prediction of vertebrate and C. elegans genes. HMMgene http://www.jcat.de/ JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage. JCat http://bioinformatics.ksu.edu/bindn/ BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs). BindN http://zlab.bu.edu/SeqVISTA/ Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister. SeqVISTA Statistics http://www.biocyc.org/ BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms) BioCyc Knowledge Library http://lorentz.immstr.pasteur.fr/nomad-ref.php Normal Mode Analysis, Deformation, and Refinement (NOMAD- Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions. NOMAD-Ref http://bioinformatics.biol.uoa.gr/PRED-TMBB/ PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods. PRED-TMBB http://wilab.inha.ac.kr/pseudoviewer2/ PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures. PSEUDOVIEWER http://www3.oup.co.uk/nar/database/a/ Molecular Biology Database Collection with links to databases with short descriptions of each. Nucleic Acids Research Database Issue http://atensembl.arabidopsis.info/ Access to the Arabidopsis thaliana genome through the Ensembl user interface. There are two independent assemblies available, one from TIGR and one from MIPS. Includes the collection of NASC insertion mutants. Arabidopsis Ensembl http://www.cisreg.ca/gsb/ Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences. Gene Set Builder http://bioinformatics.albany.edu/~cemc/ A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY. CE-MC http://tfam.lcb.uu.se/ TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments. TFAM http://psidev.sourceforge.net/ HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data. HUPO Proteomics Standards Initiative http://istech21.com/en/service/snp_a01_in.html ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary. ISTECH SNPAnalyzer http://mulan.dcode.org/ Mulan is a multiple sequence alignment tool. It employs novel algorithms such as TBA and multiTF to respectively perform alignments and discover transcription factor binding sites. Results can be viewed as dot-plots of individual sequence alignments, or dynamically browsed with the ability to zoom in from sequence conservation profiles down to the level of the individual characters of the sequence alignment. Mulan http://biocomp.bioen.uiuc.edu/oscar/ OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data. OSCAR http://www.ebi.ac.uk/intenz The goal of IntEnz is to create a single relational database containing enzyme data from three different sources: the official version of the Enzyme Nomenclature comprising recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions; Swiss Institute of Bioinformatics (SIB) Enzyme Nomenclature database (ENZYME); BRENDA, the enzyme function database which contains information on substrates, products, and inhibitors. IntEnz: Integrated relational Enzyme database http://wishart.biology.ualberta.ca/moviemaker/ MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions. MovieMaker http://www.riboclub.org/cgi-bin/RTAnalyzer/index.pl? page=rt_find RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures. RTAnalyzer http://kinefold.u-strasbg.fr/rna.html List of RNA folding servers and related web sites maintained by Herve Isambert. RNA folding Servers http://ffas.burnham.org/ The Fold & Function Assignment System (FFAS03) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. FFAS03 http://www.pathogenomics.ca/probelynx Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit. ProbeLynx http://guinevere.otago.ac.nz/mlrgd/STATS/index.html GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE, PEDEL, and DRIVeR http://bioportal.weizmann.ac.il/dipol/ The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure. Protein Dipole Server http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome List of prominent complete genomes with access to BLAST and precomputed conserved domains and protein homologs in complete genome context. Entrez Genomes http://www.zbh.uni-hamburg.de/wurst/ Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures. Wurst http://statcomp.ats.ucla.edu/ The Stat Computing Portal is a single search engine that allows you to search over 20,000 pages on statistical computing. The Stat Computing Portal is broken up into smaller portals focused on these statistical packages -- SAS, Stata, SPSS, SUDAAN, WesVar, HLM, MLwiN, S-Plus/R, Limdep, and Mplus. UCLA Statistical Computing Portal http://darwin.nmsu.edu/cgi-bin/blast_filter.cgi A tool that uses BLAST analyses to assemble a set of sequences from a single query sequence. Users can customize rules which act to filter out certain sequences from the full set of BLAST results. BLAST Filter http://pipe.scs.fsu.edu/ PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein. PI2PE http://genethics.ca/index.html The goal of this site is to serve as a clearing house for information on the social, ethical and policy issues associated with genetic and genomic knowledge and technology. Genethics.ca - The Genetics & Ethics page http://bioinformatics.ubc.ca A world-class centre of excellence for bioinformatics research and training. UBC Bioinformatics Center (UBiC) http://lowelab.ucsc.edu/snoGPS/ snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence snoGPS http://www.h-invitational.jp/ The H-Invitational Database (H-InvDB) is a human gene database containing over 20,000 cDNA clusters from multiple high- throughput cDNA sequencing projects. The website provides a genome browser, blast searching, and searching based on information such as OMIM, GO, SCOP and HUGO IDs, chromosome number, data source and feature type. There is also an online user manual, and much of the data is downloadable in both flat file and XML formats. H-Invitational Database http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc. FeatureScan http://www.ncbi.nlm.nih.gov/genome/clone/ A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information. NCBI Clone Registry http://song.sourceforge.net/ The Sequence Ontology Project aims to provide a standard vocabulary for describing biological sequences. The Sequence Ontology Project http://www.bcgsc.ca/lab/mapping/rat BAC fingerprint map of the rat genome, by Genome Sciences Centre, Vancouver. Rat BAC Physical Map http://cibex.nig.ac.jp/ The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard. CIBEX http://harvester.embl.de/ Harvester provides fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI. Harvester Health_and_Disease http://wishart.biology.ualberta.ca/basys/ BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways. BASys Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses. Viral Bioinformatics http://athena.bioc.uvic.ca/ http://www.123genomics.com/files/courses.html Links to Courses, College Degrees and Training at 123 Genomics - a Genomics, Proteomics and Bioinformatics Knowledge Base 123 Genomics: Courses, College Degrees and Training http://ps.cb.k.u-tokyo.ac.jp/ PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome. PrimerStation http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/ pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available. pknotsRG Web_Services http://globin.cse.psu.edu/enterix/ EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences. EnteriX http://www.angelfire.com/ga2/nestsite2/bioinform.html Seven interrelated modules expose the user to tools and databases currently used by researchers in molecular biology. Learn how to use NCBI resources http://genomics.senescence.info/index.html The Human Ageing Genomic Resources (HAGR) website provides tools and curated databases relevant to the genetics of human ageing. GenAge is a database of genes related to human ageing, and AnAge is a multi-species database facilitating the comparative biology of ageing. The Ageing Research Computational Tools (ARCT) is a collection of Perl modules to assist comparative genomics research. Human Ageing Genomic Resources http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml Vector Alignment Search Tool for viewing protein structure neighbours. VAST http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/ Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins. JEvTrace http://www.bchimps.bc.ca/ BC Health Information Management Professionals' Society (BCHIMPS) non-profit organization that is responsible for managing health information within BC. BCHIMPS http://pbga.pasteur.fr/GeneFizz/ GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA. GeneFizz http://www.sanger.ac.uk/Software/Artemis/ DNA sequence viewer and annotation tool; allows visualization of sequence features and results of analyses within the context of the sequence and its 6-frame translation; available for UNIX, Windows and Macintosh. Artemis http://us.expasy.org/tools/peptident.html PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data. PeptIdent http://www.imtech.res.in/raghava/bhairpred/ BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine. BhairPred http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs. PriFi http://aba.nbcr.net/ Alignment on the with an A-Bruijn Approach (AliWABA) is a web based version of a method for multiple sequence alignment that represents an alignment as a directed graph and has proved useful in aligning nucleotide and amino acid sequences that are composed of repeated and shuffled subsequences. AliWABA http://www.chra.ca/pages/01about/01about_us.html The Canadian Health Information Management Association (CHIMA) is a membership-based organization that manage the security, privacy and accuracy of patient records in hospitals across Canada. CHIMA http://ricetfdb.bio.uni-potsdam.de/ RiceTFDB(Rice Transcription Factor DataBase) is a database of sequences and alignments for transcription factors in Rice. RiceTFDB http://bioserv.rpbs.jussieu.fr/cgi-bin/PPG The Protein Picture Generator (PPG) is a tool for making pictures (and animations) of protein structures from PDB files. PPG http://www.cbs.dtu.dk/services/SignalP-2.0/ Prediction of presence and location of signal peptide cleavage sites in amino acid sequences. SignalP http://genome.ucsc.edu/cgi-bin/hgGateway? org=Rat&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the rat genome at any scale, together with dozens of aligned annotation tracks. UCSC Rat Genome Browser Gateway http://bioinformatics.org/sms2/ The Sequence Manipulation Suite is a set of tools for tasks such as sequence format conversion, sequence presentation, analysing sequence characteristics and shuffling or generating random sequences. It can be accessed over the web, or installed locally and run through a web browser. The Sequence Manipulation Suite 2 http://kinase.uhnres.utoronto.ca/CanArrays.html Contact information, availabilities and expertise of Canadian microarray centres; includes labs that supply cDNA or oligonucleotide spotted arrays and other services, and labs that can analyse RNA with Affymetrix chips. Canadian Microarray Resources General_Resources http://www.bio-itworld.com/ BIO IT technology trends & forecasts, industry news & analysis, bioinformatics and drug discovery updates. Bio-IT World http://arep.med.harvard.edu/mrnadata/mrnasoft.html Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement. AlignACE http://www.nii.res.in/searchpks.html SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains. SEARCHPKS http://nrc.bu.edu/cluster/ ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties. ClusPro http://cupsat.uni-koeln.de/ Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures. CUPSAT http://www.pathogenomics.sfu.ca/islandpath/ IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin. IslandPath Goldmines http://ecrbrowser.dcode.org/ The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented. ECR Browser http://www.enzim.hu/servers.html A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses. Institute of Enzymology Servers http://bioinfo.lifl.fr/mreps/ mreps is a tool for identifing tandemn repeats in DNA sequences. mreps http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes. AMIGene http://abcis.cbs.cnrs.fr/kindock/ KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase- ligand complexes extracted from the Protein Data Bank (PDB). KinDOCK http://www.rnabase.org/ RNAbase is a searchable and annotated database of all publicly available RNA structures. RNAbase http://molmovdb.org/ The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available. MolMovDB http://www.cellbio.unige.ch/RNAi.html T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering. TROD http://www.pir.uniprot.org/ UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt http://bindr.gdcb.iastate.edu/ZiFiT/ ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences; free registration is required. ZiFiT http://daphnia.cgb.indiana.edu/ The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for evolutionary / ecological genetics and genomics. Daphnia Genomics Consortium http://bioinformatics.bmc.uu.se/evaller/ EVALLER predicts potential protein allergenicity from primary amino acid sequence. EVALLER http://gibk26.bse.kyutech.ac.jp/jouhou/readout/ Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures. Readout http://promoterplot.fmi.ch/ PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool. PromoterPlot http://genome.ucsc.edu/cgi-bin/hgGateway?org=C. +briggsae&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the C. briggsae genome at any scale, together with dozens of aligned annotation tracks. UCSC C. briggsae Genome Browser Gateway http://www.bioinformaticssolutions.com/products/ph/index.php PatternHunter is a general purpose sequence similarity search tool for DNA and protein sequences. PatternHunter http://genesilico.pl/meta GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers. GeneSilico http://www.bcgsc.bc.ca/chinook/ Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application. Chinook http://alggen.lsi.upc.es/ ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons. ALGGEN http://www.tigr.org/tdb/tgi/plant.shtml Gene indicies for a number of plants including Arabidopsis, grape, and maize. TIGR Plant Gene Indicies Community http://genome.ucsc.edu/cgi-bin/hgGateway? org=Human&db=0&hgsid=27735471 Provides a rapid and reliable display of any requested portion of the human genome at any scale, together with dozens of aligned annotation tracks. UCSC Human Genome Browser Gateway http://bighost.area.ba.cnr.it/BIG/PatSearch/ PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices. PatSearch http://bioinfo2.ugr.es/IsoF/isofinder.html IsoFinder is a tool for the prediction of isochores for a user-supplied sequence. IsoFinder Other_Vertebrates http://knots.mit.edu/ KNOTS is a web server that detects knots in protein structures. KNOTS http://pubchem.ncbi.nlm.nih.gov/ PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem can be searched by keywords, chemical properties, and structural similarity. PubChem's chemical structure records are linked to other NCBI databases including PubMed. PubChem http://enm.lobos.nih.gov Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo. AD-ENM http://creme.dcode.org/ CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions. CREME http://140.121.196.30/remus.asp REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences. ReMus http://www.celeganskoconsortium.omrf.org/ Worldwide consortium whose ultimate goal is to produce null alleles of all known genes in the C. elegans genome; submit your gene to the knockout list. C. elegans Gene Knockout Consortium http://bioinf.cs.ucl.ac.uk/software.html A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. Servers at University College London http://bioinf.xmu.edu.cn/software/geps/geps.php Gene Expression Pattern Scanner (GEPS) is a tool for the analysis of patterns of expression in microarray data. Users can upload custom data, or can use this tool to search public data sets from GEO or GNF SymAtlas. GEPS http://www.bernstein-plus-sons.com/software/rasmol/ 3-D structure viewer, web browser helper application. RasMol http://www.flugenome.org/ FluGenome is a tool for determining lineages and genotypes of influenza A viruses. FluGenome http://www.genedb.org/ The GeneDB projects primary goal is to develop and maintain curated database resources for three organisms: Schizosaccharomyces pombe, the kinetoplastid protozoa Leishmania major, and Trypanosoma brucei. GeneDB http://www.glycosciences.de/tools/PubFinder/ PubFinder is a tool to facilitate searching through PubMed abstracts. The user chooses a set of abstracts that are representative of the subject area of their search. PubFinder then uses words from the selected abstracts to search for other papers likely belonging to the same subject area. PubFinder http://www.vessels.bwh.harvard.edu/ This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information. Defining Transcriptional Programs in Vascular Endothelium http://augustus.gobics.de/submission AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web interface, or downloaded and run locally. AUGUSTUS http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized. TFBScluster http://cbm.bio.uniroma2.it/mint/ Curated database with a focus on experimentally verified molecular interaction data collected from scientific literature. Emphasis on mammalian organisms. MINT - a Molecular INTeractions database http://bioinformatics.bc.edu/clotelab/RNALOSS/ RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures. RNALOSS http://www.ncbi.nlm.nih.gov/ NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information; est. 1988. National Center for Biotechnology Information http://biocore.unl.edu/primer/primerPI.html Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments. DePIE cDNA__EST__SAGE http://www.jenner.ac.uk/MHCPred/ Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands. MHCPred Text_Mining http://gvs.gs.washington.edu/GVS/index.jsp Genome Variation Server (GVS) is a database that provides access to human genotype data found in dbSNP, and tools for the analysis of genotype data. GVS http://blast.wustl.edu/ Washington University Basic Local Alignment Search Tool WU BLAST http://droog.mbt.washington.edu/PolyPhred.html UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use. PolyPhred http://biodata.mshri.on.ca/osprey Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows. The Osprey Network Visualization System http://compbio.cs.sfu.ca/taverna/ taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators. taveRNA Other_Molecules http://andromeda.gsf.de/wiki WikiGene is a scientific project that follows a community-based approach to collect data about genes and gene regulatory events. WikiGene http://motif.stanford.edu/distributions/3matrix/ 3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine. 3Matrix http://mrs.cmbi.ru.nl/ MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set. MRS http://math.genebee.msu.ru/~psn/ SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences. SDPpred http://metameme.sdsc.edu/ Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif. Meta-MEME Phylogeny_Reconstruction http://imgt.cines.fr/ The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user- provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences. IMGT/V-QUEST http://rosettadesign.med.unc.edu RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations. RosettaDesign http://www.transcriptome.ens.fr/doelan/ Doelan is an tool designed to monitor the quality of DNA microarray production. Doelan http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml Molecular Modelling Database of 3-D structures; experimentally determined structures only. MMDB http://psfs.cbrc.jp/tmbeta-net/ Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence. TMBETA-NET http://www.dkfz.de/spec/glycosciences.de/sweetdb/ms/ GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures. GlycoSearchMS http://sakura.ddbj.nig.ac.jp/ SAKURA is the DDBJ DNA Database Submission System. SAKURA http://bibiserv.techfak.uni-bielefeld.de/bibi/ Tools_RNA_Studio.html RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization. RNA Studio http://bioinformatics.org/vlinux/ VLinux is a bootable Linux distribution based on Knoppix. It does not require installation, and contains several bioinformatics software packages including EMBOSS, Phylip, ClustalX, HMMER and Rasmol. VLinux http://wwwmgs.bionet.nsc.ru/mgs/gnw/ Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD). GeneExpress2.1 http://genomebiology.com/researchnews/ Research news from the life sciences. Genome Biology http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides. MODPROPEP http://www.biopax.org/ The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways. BioPax Protein Fish http://caps.ncbs.res.in/harmony/ Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure. Harmony http://www.pubgene.com/public.htm Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package. PubGene http://elm.eu.org/ Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence. ELM http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/ ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots. ConPred II http://www.ncbi.nlm.nih.gov/geo/ Gene expression and hybridization array data repository; online resource for retrieval of gene expression data from any organism or artificial source. GEO - Gene Expression Omnibus http://pseudomonas.com/ This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon- based, protein-localization based, gene function category and ortholog/paralog-based information. Pseudomonas Genome Project http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank. NCBI Influenza Virus Sequence Annotation Tool http://science.bio.org/all.news.html Archived daily news source for current events in biotechnology. Science.bio.org News http://www.phosphosite.org/ PhosphoSite is a curated database of in vivo human and mouse phosphorylation sites. The database contains peptide sequences and locations within domains and motifs for the phosphorylation sites, and links to useful resources and literature references. For educational users, information extracted from the public domain is freely available. PhosphoSite http://img.jgi.doe.gov/ The Integrated Microbial Genomes (IMG) system facilitates the comparison of genomes sequenced by the Joint Genome Institute (JGI). It can be searched using keywords or BLASTp, and the gene records diplayed include biochemical properties, protein domains, chromosomal location and neighbourhood and lists of paralogues and orthologues. One can easily build a list of genomes to be considered or excluded from the search and the Phylogenetic Profiler tool allows one to refine the selection by building a list of homologues either common to or excluded from specific organisms. Integrated Microbial Genomes (IMG) http://cabio.nci.nih.gov/soap/services/index.html SOAP interfaces used to access the cancer Bioinformatics Infrastructure Objects(caBIO) funtionality. caBIO Web Services http://www.geno2pheno.org/cgi-bin/geno2pheno.pl Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs. Geno2pheno http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets. CONFAC Bioinformatics_Related_News_Sources http://taxonomy.zoology.gla.ac.uk/rod/treeview.html Generates nice graphics of trees; reads multiple tree file formats; available for download to Mac or PC. TreeView http://oligodb.charite.de/ Oligodb generates oligos suitable for expression experiments based on predicted gene transcripts from the Ensembl project. One can search for transcripts via keyword, or do a batch search by providing a list of Ensembl identifiers. Oligodb http://www.informatics.jax.org/silver/ Online version of textbook by Lee Silver. Mouse Genetics: Concepts and Applications http://www.bioinformatik.de/ Yahoo-like Webdirectory for bioinformatics. Bioinformatik http://gordion.hpc.eng.ku.edu.tr/prism/ PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions. PRISM http://www.cytoscape.org/ Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions. Cytoscape http://ffas.burnham.org/Fragnostic Fragnostic is a tool for exploring common structural elements, or fragments, between proteins which have different folds. Fragnostic http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg The Zebrafish Information Network (ZFIN). ZFIN serves as the zebrafish model organism database. ZFIN http://www.fruitfly.org/annot/apollo/ Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. Apollo Genome Annotation and Curation Tool http://www.hprd.org/ The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature. Human Protein Reference Database http://genome.ewha.ac.kr/ECgene/ASmodeler/ Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes. ASmodeler http://www.biw.kuleuven.be/logt/PHIRE.htm Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes. PHIRE http://www.nhgri.nih.gov/10001688 The haplotype map, or HapMap, is a tool that will allow researchers to find genes and genetic variations that affect health and disease. International HapMap Project http://statgen.ncsu.edu/asg/ The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer. Alternative Splicing Gallery http://opal.biology.gatech.edu/GeneMark/ The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes. GeneMark http://www.rpmpn.mcgill.ca/ A network of researchers working towards the identification, characterization and localization of every protein for every mammalian cell organelle. Montreal Proteomics Network (RPMPN) This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3. eBioinformatics http://www.ebioinformatics.org/ http://salilab.org/modeller/ Homology or comparative modeling of 3D protein structures. Modeller http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/ LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences. LowComplexity http://csbl.bmb.uga.edu/protein_pipeline An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses. PROSPECT-PSPP http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies. PMG http://www.bioperl.org/ The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. BioPerl http://tcag.bioinfo.sickkids.on.ca/ The Centre for Applied Genomics is a Canadian centre for human genome and disease research. Resources include Genomic and cDNA library screening (human, mouse, dog, pig) provided free to Canadian academic researchers with a nominal clone retrieval fee. Also: Research Genetics, NIA/NIH and RIKEN cDNAs. TCAG: The Centre for Applied Genomics, Toronto http://www.lecb.ncifcrf.gov/flicker/ Flicker provides the means to compare images from different internet sources using a java-enabled web browser. It was originally designed for the comparison of 2D gels. NCI Flicker http://genes.mit.edu/genomescan.html Incorporates protein similarity information when predicting genes; based in part on GENSCAN. GenomeScan http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html Dot plot tool with very helpful learn by example interpretations of sample outputs. Dotlet http://bioinformatics.bc.edu/clotelab/RNAbor/ RNAbor is a server for computing structural neighbors of a RNA secondary structure. RNAbor http://dictyworkbench.sdsc.edu/ Dictyostelium discoideum genome annotation and analysis portal; specialized Dictyostelium sequence and function annotaton database; the following features are available for querying: browse entire list of ORFs, view annotations, PFAM domain information, ORF details Dicty WorkBench http://cbm.bio.uniroma2.it/ispot/ iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains. iSPOT http://www.ch.embnet.org/software/BOX_form.html Printing and shading of multiple alignment files. BoxShade http://www.ensembl.org/Drosophila_melanogaster/ Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining). Ensembl Drosophila Genome Browser http://www.partigenedb.org/ PartiGeneDB is a database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data. PartiGeneDB http://gpcr.biocomp.unibo.it/biodec/ TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides. TRAMPLE http://www.ogic.ca/projects/xplormed/ XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion. XplorMed http://www.ncbi.nlm.nih.gov/BLAST/ Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST http://dscheck.rnai.jp/ dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs. dsCheck http://igs-server.cnrs-mrs.fr/phydbac/ Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes. Phydbac2 http://genereg.ornl.gov/webgestalt/ WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected. WebGestalt http://biomint.pharmadm.com:8090/protop/bin/bmsynonyms.pl Gene and Protein Synonym DataBase (GPSDB) is a collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user- selected terms. GPSDB http://www.gene-regulation.com Access to databases, programs and papers related to gene regulation. Gene Regulation http://zlab.bu.edu/cluster-buster/ Cluster Buster is a tool that finds clusters of pre- specified motifs in DNA sequences. Cluster Buster http://www.cs.ubc.ca/~tmm/papers/sj/ SequenceJuxtaposer is a tool for visualizing and comparing biomolecular sequences. Uses a visualization technique called accordion drawing that allows users to zoom into regions of interest in alignments. SequenceJuxtaposer http://www.gene-regulation.com/pub/programs.html#matinspector Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non- commercial use. MatInspector http://ekhidna.biocenter.helsinki.fi/poco/ POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented. POCO http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences. RNAhybrid http://www.fugu-sg.org/ Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST. IMCB - Fugu Genome Project http://rdp.cme.msu.edu/ Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download. Ribosomal Database Project http://stitchprofiles.uio.no/ Stitchprofiles.uio.no is a server that performs web- based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server can also plot the classical melting curves, probability profiles, and temperature profiles. Stitchprofiles.uio.no http://babelomics.bioinfo.cipf.es/fatigoplus/cgi-bin/ fatigoplus.cgi FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes. FatiGOplus Expression http://ibivu.cs.vu.nl/programs/popscompwww/ POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed. POPSCOMP http://bibiserv.techfak.uni-bielefeld.de/jpredictor/ jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence. jPREdictor http://jphmm.gobics.de/ Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence. jpHMM http://bioserv.rpbs.jussieu.fr/Help/PCE.html PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package. PCE http://biosrv1.bmi.ac.cn/RSRE/ RNA Structural Robustness Evaluator (RSRE) is a tool for RNA structural robustness evaluation. RSRE http://www-cryst.bioc.cam.ac.uk/~joy/ JOY is a program for displaying 3D structural information in a multiple sequence alignment. JOY http://funshift.cgb.ki.se/ FunShift is a database that stores Pfam subfamily classification for protein domain families and analyses them for functional changes using evolutionary substitution rates and conservation shifts. FunShift http://redpoll.pharmacy.ualberta.ca/vadar/ Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data. VADAR http://www.ncbi.nlm.nih.gov/Sequin/index.html Desktop tool developed by the NCBI for editing, annotating and submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ, EMBL or GenBank). Sequin http://viscose.ifg.uni-muenster.de/ VisCoSe (Visualization and Comparison of consensus Sequences) is a web based tool that takes a set of sequences (aligned or unaligned) and calculates a consensus sequence and the conservation rates for the sequence alignment, producing an easy to interpret visualization as output. One can also compare and visualize a set of consensus sequences generated from several sequence sets. VisCoSe http://bibiserv.techfak.uni-bielefeld.de/dialign/ Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities. DIALIGN http://umber.sbs.man.ac.uk/cgi-bin/neil/ntfront.pl FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions. FAN http://wishart.biology.ualberta.ca/PlasMapper/index.html Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats. PlasMapper http://140.113.239.131/RE-MUSIC/ RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression contraints. RE-MuSiC http://toolkit.tuebingen.mpg.de/index.php?view=hhsenser HHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies. HHsenser http://asia.genesilico.pl/colorado3d/ COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL. COLORADO-3D http://bibiserv.techfak.uni-bielefeld.de/rnamovies/ RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data. RNA Movies http://smart.embl-heidelberg.de/ SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. SMART http://lnatools.com/ LNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, real time PCR, and SNP genotyping. LNAtools http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. PROFEAT http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/ Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3' terminus to look for the patterns. BEARR http://whipple.cs.vt.edu:8080/virgo Virtual Gene Ontology (VIRGO) provides gene function predictions for yeast and human by constructing a functional linkage network (FLN) from gene expression and molecular interaction data. VIRGO then labels genes in the FLN with their annotations from Gene Ontology, and systematically propagates these labels across the FLN in order to predict the functions of unlabelled genes. VIRGO http://www.genecards.org/ Database of human genes, their products, and involvement in diseases; free for non-commercial use, but users should also read the Terms of Use for this site. GeneCards http://www.dddc.ac.cn/tarfisdock/ Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets. TarFisDock http://www.tigr.org/tdb/bac_ends/rat/bac_end_intro.html TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; BACs are same as those fingerprinted by Genome Sciences Centre, Vancouver. Rat BAC Ends http://antigen.i2r.a-star.edu.sg/multipred/ MULTIPRED is a tool for mapping T-cell epitopes by prediction peptides that bind to human leukocyte antigen (HLA) class I A2, A3 and class II DR supertypes. MULTIPRED http://www.jprogo.de/index.jsp JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. JProGO http://www.phrap.org/ UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non- commercial use. Phred/Phrap/Consed System http://tico.gobics.de/ TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER. TiCo http://prospector.ucsf.edu/ Various tools used for sequence database mining in connection with mass spectrometry experiments. ProteinProspector http://path-a.cs.ualberta.ca/ Pathway Analyst (Path-A) predicts and annotates pathways present in the query organism and provides a browsable database of ten currently supported metabolic pathways. Path-A can also take as input a list of protein sequences and identify those sequences that are likely to participate in the supported metabolic pathways. Path-A http://stat.genopole.cnrs.fr/websic/ Scan Inverse Complementary (SIC) provides a tool for detecting short inverted segments in a DNA sequence. WebSIC http://www.esat.kuleuven.ac.be/inclusive INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. INCLUSive http://genome.ucsc.edu/cgi-bin/hgGateway? org=SARS&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the SARS genome at any scale, together with dozens of aligned annotation tracks. UCSC SARS Genome Browser Gateway http://www.mysql.com MySQL is the world's most popular Open Source Database, designed for speed, power and precision. MySQL http://pheps.orgchm.bas.bg/home.html pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file. PHEPS http://www.genoscope.cns.fr/agc/tools/micheck/ MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes. MICheck http://www.ebi.ac.uk/proteome/ The Proteome Analysis Database at EBI provides statistical and comparative analyses of the predicted proteomes of organisms for which there are fully-sequenced genomes. Proteome Analysis at EBI http://www.charite.de/bioinf/strap/ The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included. STRAP http://ecoli.bham.ac.uk/ comprehensive guide to information relating to E. coli; home of Echobase: a database of E. coli genes characterized since the completion of the genome E.Coli Index http://www.tigr.org/tigr-scripts/magic/r1.pl Tool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) databases. Resourcerer http://neuroproteomics.scs.uiuc.edu/neuropred.html NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications. Neuropred http://www.tigr.org/tdb/tgi/fungi.shtml Gene indicies for a number of fungal/yeast organisms such as Schizosaccharomyces pombe and Saccharomyces cerevisiae. TIGR Fungal Gene Indices http://scansite.mit.edu/ Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains. Scansite http://gelbank.anl.gov/ GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available. GELBANK http://array.mbb.yale.edu/analysis/ ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering. ExpressYourself http://wolfpsort.org/ WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT http://biobases.ibch.poznan.pl/ncRNA/ Non-translatable RNA transcripts that appear to work at the RNA level. Non-Coding RNA database http://protevo.eb.tuebingen.mpg.de/hhpred Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models. HHpred http://cl.sdsc.edu/ce.html Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank. Combinatorial Extension of the Optimal Path http://www.linux.org/ Comprehensive information and resources about the Linux Operating System. Linux Online http://www.dhgp.de/ethics/index.html Findings of several scientific meetings held to evaluate the requirement for further research into the ethical implication of human genome science from the German Human Genome Project are summarized here. German Human Genome Project - Ethics http://www.imtech.res.in/raghava/eslpred/ ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties. ESLpred http://www.ncbi.nlm.nih.gov/SNP/ Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI. dbSNP http://www.ncbi.nlm.nih.gov/mhc/sbt.cgi?cmd=main The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments. SBT Interface - dbMHC http://drtf.cbi.pku.edu.cn/ Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from <i>japonica</i> and <i>indica</i> rice genomes. DRTF http://ligin.weizmann.ac.il/space/ SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes. SPACE 2-D_Structure_Prediction Education http://cismols.cchmc.org/ CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions. CisMols http://www.cbs.dtu.dk/services/NetGene2/ The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA. Netgene2 Directories_and_Portals http://www.rodentia.com/wmc/ Numerous links to Internet resources for mouse and rat research; resource categories include genome, cell, organ, organism, laboratory etc. Whole Mouse Catalog http://discover.nci.nih.gov/textmining/ MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords. MedMiner http://www.pathblast.org/ PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein- protein interation network specified by the user. PathBLAST https://prosa.services.came.sbg.ac.at/prosa.php ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling. ProSA-web Human_Genome http://biodev.hgen.pitt.edu/enologos/ enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements. enoLOGOS http://evolution.berkeley.edu/ A fantastic site for teaching/understanding evolution. Understanding Evolution http://www.nii.res.in/searchgtr.html SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs. SEARCHGTr http://www.fruitfly.org/ Good entrez to fly genome resources. Berkeley Drosophila Genome Project http://bioinfow.dep.usal.es/apid/ Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT. APID http://www.kazusa.or.jp/codon/ Find GC content and frequency of codon usage for any organism that has a sequence in GenBank. Codon Usage Database http://www.poxvirus.org/ Includes poxvirus genomic sequences; annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; literature resource; repository of poxvirus species and strains; discussion forum. Poxvirus Bioinformatics Resource Center http://toolkit.tuebingen.mpg.de/index.php?view=hhrep HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs). HHrep http://genome.imim.es/astalavista/ AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets. AStalavista http://blocks.fhcrc.org/ The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions. Blocks WWW Server http://bioinformatics.lcd-ustc.org/sumosp/prediction.php SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO). SUMOsp Utilities http://meme.nbcr.net/meme/intro.html MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains. MEME http://insilico.ehu.es/ Provides tools for theoretical PCR amplification, AFLP- PCR and PFGE with all up-to-date public complete bacterial genomes (300+ genomes available). In silico experiments with complete bacterial genomes http://robotics.stanford.edu/~xsliu/MDscan/ Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites. MDscan http://www-unix.mcs.anl.gov/compbio/index.html Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available. Argonne National Laboratory - Computational Biology Databases Sequence_Data http://www.expasy.ch/swissmod/SWISS-MODEL.html Automated protein modelling server. Swiss Model http://www.phylofoot.org/consite/ Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally- confirmed binding profiles. Consite http://sunserver.cdfd.org.in:8080/protease/PAR_3D/index.html PAR-3D (Protein Active site Residues - 3D structural motif) uses a structure-based approach for predicting function. Using 3D structural motifs defined for different classes of proteases, glycolytic pathway enzymes and metal-binding sites, PAR-3D predicts probable active site residues. PAR-3D http://bioinformatics.bc.edu/clotelab/BTW/ Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time. BTW http://oblab.cs.nchu.edu.tw:8080/WebSDL/ NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants. NTMG http://bioserv.rpbs.jussieu.fr/ Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP). RPBS http://www.sbg.bio.ic.ac.uk/~3dpssm/ Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information. 3D-pssm http://igs-server.cnrs-mrs.fr/elnemo/start.html ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein. ElNemo http://www.microbial-pathogenesis.org/stickwrld/ The Multiple Alignment Variation Linker (MAVL) examines a pre-aligned set of nucleotide or protein sequences and detects positive and negative interpositional correlations. The results can then be viewed as a StickWRLD representation. MAVL/StickWRLD http://www.magma-fgcz.unizh.ch/pages/loginuser.jsf MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download. MAGMA http://dip.doe-mbi.ucla.edu/ The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries. DIP http://bioinformatics.ubc.ca/resources/links_directory/ The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee. Bioinformatics Links Directory http://compbio.ornl.gov/Grail-1.3/ Grail is a suite of tools which recognizes sequence features like promoters, exon candidates, simple repeats and complex repetitive elements. It also models genes based on the exon candidates. Grail http://www.ncbi.nlm.nih.gov/UniGene/ Non-redundant sets of expressed genes; each UniGene cluster contains sequences, model organism homologs, map and expression information. UniGene http://www.perlmonks.org/ Perl community site Perl Monks http://www.mutdb.org/ MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers. MutDB http://xray.bmc.uu.se/embo/structdb/links.html Detailed compendium of links to structure databases, viewers, tools. Practical Structural Databases http://www.basic.northwestern.edu/biotools/OligoCalc.html OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5 and 3 chemical modifications and predict potential hairpin loop formation. OligoCalc http://www.rostlab.org/services/CHOP/ CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database. CHOP http://us.expasy.org/spdbv/ Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial *Molecular Modeling for Beginners* is a must (listed on this page). Swiss-PdbViewer http://www.ebi.ac.uk/arrayexpress/ Public repository for microarray based gene expression data; contains several curated gene expression datasets. ArrayExpress http://sdmc.lit.org.sg/ERE-V2/index Dragon Estrogen Response Element Finder (DEREF) allows the discovery of transcription factor binding sites (TFBS) in vertebrate genomic sequences. DEREF http://pupasview.bioinfo.ochoa.fib.es/ PupasView takes a single gene identifier as input and reports SNPs that have the potential to affect phenotype. In addition to looking for potential amino acid changes, PupaSNP also searches for SNPs with the potential to affect proper transcription, such as those in intron/exon boundaries, predicted transcription factor binding sites, and exonic splicing enhancers. PupasView http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable. CD-Search http://genopole.toulouse.inra.fr/bioinfo/Iccare/ The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism. Iccare Bio-X_Programming_Tools http://mgc.nci.nih.gov/ Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible. Mammalian Gene Collection Proteomics Tutorials_and_Directed_Learning_Resources http://bips.u-strasbg.fr/PipeAlign/ PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed. PipeAlign http://www.bcgsc.ca/gc/bomge/sockeye/ Sockeye is a visualization tool allowing one to assemble and analyze genomic information in a three dimensional workspace. It can be used to view features at various levels, ranging from SNPs to karyotypes. Sockeye displays genomic features along tracks, and links to the Ensembl database. Sockeye http://biophysics.cs.vt.edu/H++ H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures. H++ http://www.ornl.gov/TechResources/Human_Genome/ links.html#informatics Large directory of online resources. Links to the Genetic World http://pknot.life.nctu.edu.tw/ pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB. pKNOT Web_Development http://www.cbs.dtu.dk/services/GenePublisher GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data. GenePublisher http://genes.mit.edu/GENSCAN.html Identification of complete gene structures in genomic DNA. GENSCAN http://www-bs.informatik.uni-tuebingen.de/SVMHC/ SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding. SVMHC http://bioinformatics.upmc.edu/GE2/GEDA.html The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization. Gene Expression Data Analyzer http://www.biorag.org/pathway.html Pathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses. Pathway Miner http://bioinfo.cis.nctu.edu.tw/service/gprm/ Genetic Programming for RNA Motifs (GPRM) finds common secondary structure elements in a set of unaligned RNA sequences. GPRM http://www.psc.edu/biomed/genedoc/ Multiple sequence alignment editor, analyser and shading utility for Windows. GeneDoc http://www.gene-regulation.com/pub/databases.html#transfac Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non- commercial use. TRANSFAC http://www.mged.org Group facilitating the development of an international repository for gene expression data and the experimental and database standards required for such an endeavour. Microarray Gene Expression Database http://t.caspur.it/ASPIC/ Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations. ASPic http://satellog.bcgsc.ca/ Satellog is a database for the identification and prioritization of satellite repeats in disease association studies. Satellog http://bioinfo.ebc.ee/snpmasker/ SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design. SNPmasker Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. EMBOSS http://cbrmain.cbr.nrc.ca/EMBOSS/ http://glinka.bio.neu.edu/StSNP/index_2006.html StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks. StSNP This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools. http://protevo.eb.tuebingen.mpg.de/toolkit/index.php? view=search Bioinformatics Toolkit http://bioinformatics.univ-reunion.fr/PBE/ Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database. PBE http://us.expasy.org/tools/ Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more. ExPASy Proteomics tools http://cubic.bioc.columbia.edu/eva/ EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers. EVA http://icb.med.cornell.edu/crt/RbDe/index.xml Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features. RbDe http://prosightptm2.scs.uiuc.edu/ ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the &apos;Top-Down&apos; tandem mass spectrometry (MS/MS) approach. ProSight PTM http://uprobe.genetics.emory.edu/ The Universal Probes (U-Probe) project provides access to a database of pre-computed hybridization-based probes. The probes are based on highly conserved sequences from multiple sequenced species, and can be used to screen genomic libraries for which there is a lack of available species-specific data. The database can be searched on the website, or complete copies can be downloaded. The computer scripts and experimental protocols used in the project are also available for download. Universal Probes http://gibk26.bse.kyutech.ac.jp/jouhou/shandar/netasa/qgrid/ Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins. Qgrid http://phylemon.bioinfo.cipf.es/cgi-bin/tools.cgi Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon http://www.eurekalert.org/bysubject/biology.php Daily news updates on science, medicine, health, and technology. Eureka Alert http://www.ebi.ac.uk/IPI/ IPI provides a top level view of the human, mouse and rat proteome data found in Swiss-Prot, TrEMBL, RefSeq and Ensembl. IPI - International Protein Index http://fraenkel.mit.edu/webmotifs/ WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results. WebMOTIFS http://gridgrinder.sourceforge.net/ Software for microarray image analysis. GridGrinder http://bmerc-www.bu.edu/psa/request.htm Prediction of probable secondary structures and fold- class; good for visualizing amphipathic helices, where present. PSA http://www.charite.de/bioinf/tgge/ TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping. TGGE-STAR http://foldoc.doc.ic.ac.uk/foldoc/ FOLDOC (Free Online Dictionary of Computing) is a good place to look up meanings of computer jargon. FOLDOC - Computing Dictionary http://bioinformatics.bc.edu/clotelab/transFold transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments. transFold http://mendel.imp.ac.at/dout/ Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences. DOUTfinder http://bip.umiacs.umd.edu:8080/ BioInformatics Pipeline Alternative Splicing Services (BIPASS) provides access to alternative splicing information extracted from various public databases and allows users to submit their own transcript and genome sequences for alternative splicing predictions. BIPASS http://biomoby.org/ BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery. BioMoby http://molgen.biol.rug.nl/websoftware/projector2/ Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps. Projector 2 http://manaslu.aecom.yu.edu/loopred/ ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop. ArchPred http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/ rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS). rMotif http://goblet.molgen.mpg.de/ GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted. GOblet http://its2.bioapps.biozentrum.uni-wuerzburg.de/ The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre- calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy. ITS2 http://www.tigr.org/tdb/tgi/protist.shtml Gene indices for various protists including Trichomonas vaginalis, Trypanosoma brucei, and Dictyostelium discoideum. TIGR Protist Gene Indices http://imgen.ccbb.pitt.edu/sop3v2/ SOP3v2 takes a list of gene names, a list of reference sequence IDs or a chromosomal location as input and provides a set of PCR and sequencing primers as output. These primers are optimized for sequence-based genotyping assays. SOP3v2 http://dialign.gobics.de/chaos-dialign-submission The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment. CHAOS/DIALIGN WWW server Functional_RNAs http://berry.engin.umich.edu/gene2oligo/ Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR). Gene2Oligo http://www.ensembl.org/Anopheles_gambiae/ This site presents the tenfold whole genome shotgun assembly of the PEST strain of anopheles gambiae, as prepared by The International Anopheles Genome project. Ensembl Mosquito Genome Browser http://www.gelscape.ualberta.ca/ GelScape is a platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank's repository. GelScape and GelBank http://www.humgen.umontreal.ca/en/ Access to a comprehensive international database on the legal, social and ethical aspects of human genetics. HumGen http://gemdock.life.nctu.edu.tw/3D-partner/vers1/index.php 3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes. 3D-partner http://ProKware.mbc.nctu.edu.tw/ ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only. ProKware http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program. Primer Z http://rulai.cshl.org/tools/FirstEF/ First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. FirstEF Gene_Prediction http://darwin.uvigo.es/software/prottest_server.html? ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. ProtTest http://research.i2r.a-star.edu.sg/FIE2.0/ 5' end Information Extraction v2 (FIE2) identifies and extracts nucleotide sequence around the promoter region of genes and their translation initiation sites (TIS). User can search by gene/ protein name or Locus ID. FIE2.0 http://myhits.isb-sib.ch The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users. MyHits http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/ ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes. ARGO http://correlogo.abcc.ncifcrf.gov/ CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated. CorreLogo http://trantor.bioc.columbia.edu/Target_Explorer/ Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required. Target Explorer http://202.54.26.221/dynavac/ DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences. DyNAVacS http://bioportal.weizmann.ac.il/tracts/tracts.html TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information. TRACTS http://igs-server.cnrs-mrs.fr/Caspr/index.cgi CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T- COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model. CaspR C-Cplusplus http://baboon.math.berkeley.edu/~syntenic/slam.html SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non- coding sequences). SLAM http://www.genome.gov/page.cfm?pageID=10001674 Lists of genome-related sites maintained by the NHGRI on behalf of the International Human Genome Sequencing Consortium. Genome Hub http://us.expasy.org/prosite/ Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase. PROSITE http://www.ensembl.org/Homo_sapiens/ Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes; uses NCBI assembly. Ensembl Human Genome Browser 3-D_Structure_Prediction http://mendel.berkeley.edu/dog.html The dog genome project is a collaborative study aimed at producing a map of all of the chromosomes in dogs, which can be used to map the genes causing disease and those genes controlling morphology and behavior. The Dog Genome Project http://www.pdg.cnb.uam.es/eva/con/index.html EVAcon automates the continuous evaluation of inter- residue contact prediction servers. Results can be viewed statically or dynamically generated. EVAcon http://www.w3.org/ The world wide web consortium. Keep up to date with new internet standards. w3c.org http://www.cgl.ucsf.edu/Research/genentech/canpredict/ CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations. CanPredict http://dbb.nhri.org.tw/primer/ Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences. PDA http://www.oreganno.org The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations. ORegAnno http://biowulf.bu.edu/MotifViz/ MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum. MotifViz Mapping_and_Assembly http://www.ebi.ac.uk/clustalw/ Standard multiple sequence alignment. ClustalW http://miracle.igib.res.in/quadfinder/ QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences. QuadFinder http://isacgh.bioinfo.cipf.es/ ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package. ISACGH http://hydra.icgeb.trieste.it/~kristian/dna/ DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database. DNAtools http://caps.ncbs.res.in/scanmot/scanmot.html SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs. SCANMOT http://www.sanger.ac.uk/Users/td2/eponine/ Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy. Eponine http://us.expasy.org/tools/scanprosite/ ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs. ScanProsite http://www.igb.uci.edu/servers/psss.html SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta- residue and beta-strand pairings, amino acid contact maps, and tertiary structure. SCRATCH http://bioinfo3.noble.org/miRU.htm miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant- specific gene data sets to predict potential target genes. miRU http://genomics14.bu.edu:8080/MuPlex/MuPlex.html Multi-Objective Multiplex PCR Assay Design (MuPlex) is a tool to assist in the design of multiplex PCR assays. MuPlex takes a set of DNA sequences and other experimental information as input and provides a set of multiplex PCR assays intended to cover as many of the user-supplied sequences as possible. MuPlex http://www.isrec.isb-sib.ch/madap/ MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5&apos; and 3&apos;ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example). MADAP http://discover.nci.nih.gov/gominer/ GoMiner organizes and allows the visualization of large sets of genes based on Gene Ontology classifications. GoMiner http://www.receptors.org/NR/servers/html/ NRSAS Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors. http://www.genmapp.org/ GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways. GenMAPP http://genomics10.bu.edu/terrence/gems/ GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program. GEMS http://scmd.gi.k.u-tokyo.ac.jp/ The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided. SCMD http://soap.bind.ca/ BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API). BIND SOAP http://mbgd.genome.ad.jp/ MBGD is a database for comparative analysis of completely sequenced microbial genomes using orthologue identification, paralogue clustering, motif analysis and gene order comparison. Microbial Genome Database http://dousta.umsl.edu/cgi-bin/primaclade.cgi Primaclade accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers that will bind across the alignment. Primaclade http://www.genomenewsnetwork.org/resources/glossary/ A glossary of Genomics-related terms from the Genome News Network. GNN's Genomics Glossary http://pdw-24.ipk-gatersleben.de:8080/VOMBAT/ VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees. VOMBAT http://pymol.sourceforge.net/ PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. PyMOL http://binf1.chem.mq.edu.au:8081/asgs/ Alternative Splicing Graph Server (ASGS) reads a GFF formatted file for a single gene and creates a splicing graph generated as a directed acyclic graph from the transcript information in the GFF file. ASGS http://www.conifergdb.org/software/wtm1.0/ WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3&apos; and 5&apos; termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails. WebTraceMiner DNA http://bioweb.pasteur.fr/seqanal/motif/hmmer-uk.html HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER http://www.phylo.org/ The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software. CIPRes http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constraints may also be specified, including the inclusion or exclusion of certain amino acids or protease sensitive sites. LINKER http://www.pathogenomics.bc.ca/phyloBLAST/ BLAST a protein sequence, then perform automated phylogenetic analysis on hits or on uploaded sequences; PHYLIP-based analyses. PhyloBLAST Domains_and_Motifs http://www.ensembl.org/Multi/martview The Ensembl EnsMart Genome Browser (MartView) is a tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface MartView allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats. MartView http://www.rnasoft.ca/ Software for RNA/DNA secondary structure prediction and design RNAsoft http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html Dotter is a dot-matrix program with interactive greyscale rendering for genomic DNA and protein sequence analysis. Dotter http://public-1.cryst.bbk.ac.uk/cdweb/html/ A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results. DICHROWEB http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.html INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. INFO-RNA Splicing http://biryani.med.yale.edu/karma/cgi-bin/mysql/karma.pl KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology. KARMA http://coco.protein.osaka-u.ac.jp/isotopica/ Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/ RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available. ISOTOPICA http://www.brain-map.org The Allen Brain Atlas (ABA) project has developed a web- based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region. Allen Brain Atlas http://www.bioinf.med.uni-goettingen.de/services/deep/ DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example). DEEP http://interolog.gersteinlab.org/ Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast. Interolog/Regulog Database http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top- scoring genotype. An alignment tool is also available. Genotyping - NCBI http://www.asicb.com/ The Association for Studies in Computational Biology (ASICB) website is a Bioinformatics portal with a focus on news and initiatives in India. The Knowledge Base section of the website has great summaries of key topics in bioinformatics ranging from important algorithms to descriptions of common lab techniques. The Resources section also includes listings of important Bioinformatics journals and books. Association for Studies in Computational Biology http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf). Frog http://www.imb-jena.de/IMAGE_AA.html Includes chemical structures and properties, solvent accessibility, post-translational modifications, and more; with references. The Amino Acid Repository http://www.scmbb.ulb.ac.be/pathfinding/ The Metabolic PathFinding website takes a source and a target metabolic node as input and finds the shortest path between them in a graph based on the reactions and compounds from the KEGG LIGAND database. Various types of input can be provided, including LIGAND database identifiers and EC numbers. The web tool employs two selectable methods to filter out pathways going through highly connected compounds such as water . Metabolic PathFinding http://www.ysbl.york.ac.uk/sgTarget/ sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties. sgTarget http://www-micrel.deis.unibo.it/~tom/ Transcriptomics of OMIM (TOM) searches for candidate disease genes using user supplied genomic loci. Candidate disease genes are then prioritized using co-expression patterns from public gene expression datasets and functional gene ontology annotations. TOM http://bioinfo.csie.ncu.edu.tw/ProSplicer/ Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants. ProSplicer http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts. FrameD Sequence_Comparison http://www.postgresql.org/ PostgreSQL is a sophisticated Object-Relational DBMS, supporting almost all SQL constructs, including subselects, transactions, and user-defined types and functions. It is the most advanced open-source database available anywhere. PostgreSQL http://bibiserv.techfak.uni-bielefeld.de/e2g/ E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre- computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe. E2G http://proteminer.csie.ntu.edu.tw/ ProteMiner-SSM searches the PDB for proteins with similar tertiary substructures to one specified by the user. A filtering process is used to significantly speed up the analysis. ProteMiner-SSM http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues. GeneHub-GEPIS http://www.tbi.univie.ac.at/~ivo/RNA/ Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Vienna RNA Package http://medock.csie.ntu.edu.tw/ MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites. MEDock http://bioinfo.csie.ncu.edu.tw/%7Ernamst/ RNA Motif Search Tool (RNAMST) is a tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences. RNAMST http://www.biolinux.org/ A resource for pre-compiled linux RPM files (easy-to- install packages) of popular bioinformatics tools. Tools available for download include Clustal W, EMBOSS, PHYLIP and BLAST. BioLinux http://www.cmbi.ru.nl/MGV/ Tool for visualization of microbial genomes. Chromosome wheels and linear genome maps with user specified features/color coding can be generated interactively. Graphics are created in SVG format. Microbial Genome Viewer http://www.colorbasepair.com/index.html On-line bioinformatics resources including links to news, forums, tutorials, and jobs. Color Base Pair http://genes.cs.wustl.edu/ Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan. Twinscan http://www.tigr.org/tdb/tgi.shtml TIGR Gene Indices An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices. http://www.gopubmed.org/ GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms. GoPubMed http://compareprospector.stanford.edu/ Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species. CompareProspector http://bio.cse.psu.edu/ PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences. PipMaker http://www.brenda.uni-koeln.de/ Information about reaction and specificity, post- translational modifications, structure, stability, and references to other databases; free for academics. BRENDA - The Comprehensive Enzyme Information System http://www.ncbi.nlm.nih.gov/Structure/ Good starting point with links to databases and tools. NCBI Structure Group http://cubic.bioc.columbia.edu/services/tmh_benchmark/ The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods. TMH Benchmark http://wego.genomics.org.cn/cgi-bin/wego/index.pl Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram. WEGO http://cluster.physics.iisc.ernet.in/ff/ FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against. FF - Fragment Finder http://biominer.bime.ntu.edu.tw/magiicpro/ MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented. MAGIIC-PRO http://taverna.sourceforge.net/ Taverna is a tool for creating and running bioinformatics workflows. Taverna http://www.doaj.org/ The Directory of Open Access Journals provides a listing of open-access journals and a searchable database of article abstracts from them. It aims to incorporate journals from all subjects and languages. Directory of Open Access Journals http://www.pazar.info/ PAZAR is an open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of gene expression. PAZAR http://appserver.wustl.edu:8080/webtools_v4_2/PromoterSearch.do Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors. PAP http://conreal.niob.knaw.nl/ CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences. CONREAL http://bioinfo.crs4.it/AH2.0/ AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output. AntiHunter 2.0 http://java.sun.com/ The source for java technology. java.sun.com http://www.flyreg.org/ Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila. Drosophila DNase I footprint database http://as2ts.llnl.gov/AS2TS/as2ts.html The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling. AS2TS http://www.cdfd.org.in/predictregulon/ PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes. PredictRegulon http://www.dkfz-heidelberg.de/spec/aismig AISMIG (An Interactive Server-side Molecule Image Generator) is a tool for generating and visualizing high resolution 3D images from PDB structure files. AISMIG http://mscan.cgb.ki.se/cgi-bin/MSCAN MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences. MSCAN http://www.predictprotein.org PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e- mail. PredictProtein http://www.gnu.org/software/polyxmass/ Polyxmass is collection of programs and libraries that constitute a data simulation and analysis framework for mass spectrometry. GNU polyxmass http://www.cprmap.com Clinical Proteomics Research Map (CPRMap) is dedicated to provide web information on clinical proteomics technologies and its applied proteomics. CPRMap http://gba.cbi.pku.edu.cn The GBA Server is an EST-based gene expression profiling and analysis platform. It implements the GBA (Guilt-by-Association) algorithm and, given a UniGene cluster, can be used to find genes with similar expression patterns. GBA Server http://race.unil.ch/ RACE (Remote Analysis Computation for gene Expression data) is a collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE http://pir.georgetown.edu/ PIR is an integrated bioinformatics resource. The Protein Sequence Database (PSD), a functionally annotated database of protein sequences, is located at PIR. PIR - Protein Information Resource http://www.ebi.ac.uk/asd/ Access to the AltSplice, AltExtron and AEdb databases. Alternative Splicing Database (ASD) Project http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping. SNP Cutter http://blast2srs.embl.de/ BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches. BLAST2SRS http://fred.bioinf.uni-sb.de/sepacs.html SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles. SEPACS http://redfly.ccr.buffalo.edu/?content=/search.php Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct. REDfly http://kinefold.u-strasbg.fr/ Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots. Kinefold http://cic.cs.wustl.edu/RNA/ Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences. ILM http://plntfdb.bio.uni-potsdam.de/v1.0/ Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST. PlantTFDB http://pongo.biocomp.unibo.it/pongo PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP. PONGO http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome. RF_DYMHC http://selecton.bioinfo.tau.ac.il/ Selecton is a server for the identification of site- specific positive selection and purifying selection. Selecton http://rebase.neb.com/rebase/rebase.html The Restriction Enzyme Database, a collection of information about restriction enzymes and related proteins. REBASE http://bioinformatics.ubc.ca/genecomber/index.php GeneComber is an ab initio gene prediction tool developed at the UBC Bioinformatics Centre. It integrates results from two externally developed gene finders and operates on the premise that if these two gene finders agree on a prediction, we can be more confident in the prediction. GeneComber http://www.mrc-lmb.cam.ac.uk/pubseq/ UNIX-based tools for sequence assembly, mutation detection and sequence analysis; free for non-commercial use. Note that Staden development and support have ceased due to lack of funding, despite widespread use. Staden Package http://staff.vbi.vt.edu/pathport/services/ The PathPort project at the Virginia Bioinformatics Institute (VBI) has implemented a number of web-services that provide the core data access and analysis tools capabilities for the system. VBI PathPort project services http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi- bin/EuGeneHom.pl EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb. EUGENE'HOM http://genetrail.bioinf.uni-sb.de/index.php GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes. GeneTrail http://fasta.bioch.virginia.edu/crp/ Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated. CRP http://pdg.cnb.uam.es/~txemago/TSEMA/ The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families. TSEMA http://www.sanger.ac.uk/Projects/S_pombe/ Schizosaccharomyces pombe Genome Sequencing Project. S. pombe genome http://www.predisi.de/ PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets. PrediSi http://ice.bcgsc.bc.ca/ Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver. iCE - internet Contig Explorer 3-D_Structure_Comparison http://coot.embl.de/pal2nal/ PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated. PAL2NAL http://molprobity.biochem.duke.edu/ MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes. MOLPROBITY http://hgvbase.cgb.ki.se/ Human Genome Variation database - curated; attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes. HGVbase http://bioinformatics.bc.edu/clotelab/DiANNA/ DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand. DiANNA http://www.psort.org/ PSORT.org provides links to the PSORT family of web- based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction. PSORT.org http://www.genomicseducation.ca/ Aimed to keep the general public informed about the science, technology and issues connected with genomics and proteomics. Genome British Columbia's Learning Centre http://robetta.bakerlab.org/ The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations. Robetta http://www.glycosciences.de/sweetdb/start.php? action=form_shift_estimation GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure. GlyNest and CASPER http://www.repeatmasker.org/ Screens a DNA sequence against a library of repetitive elements; returns a masked query sequence and a table annotating the masked regions. RepeatMasker http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/ RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user. RECON Literature http://www.genomenewsnetwork.org/resources/sequenced_genomes/ genome_guide_p1.shtml The Quick Guide includes descriptions of more than 150 organisms and has links to sequencing centers and scientific abstracts. A Quick Guide To Sequenced Genomes http://sdmc.lit.org.sg/promoter/dragonGSF1_0/genestart.htm Dragon Gene Start Finder (DGSF) predicts promoters and transcription start sites (TSS) within CpG islands for mammalian DNA sequences. DGSF http://cubic.bioc.columbia.edu/services/NORSp/ NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins. NORSp http://www.pubmedcentral.gov/ PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature. PubMed Central http://bioinformatics.org/ Bioinformatics.org was founded to facilitate interaction between established and aspiring bioinformatics researchers. The website provides many resources, including project hosting, online databases and analysis tools, and several forums and discussion groups. The Bioinformatics Organization, Inc. http://www.sghms.ac.uk/depts/phs/staff/jmb/pbstnote.htm Brief descriptions of statistical concepts and methods often combined with clinical/medical examples. Statistics Notes in the British Medical Journal Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto- Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required. http://vortex.cs.wayne.edu/Projects.html Onto-Tools http://www.proteus.cs.huji.ac.il/index.php ProTeus (Protein Terminus) is an archive of functional signatures in protein termini ProTeus http://www.iscb.org/ Scholarly society dedicated to advancing the scientific understanding of living systems through computation; emphasis is on the role of computing and informatics in advancing molecular biology. International Society for Computational Biology http://genomecanada.ca/ The primary funding resource relating to genomics and proteomics in Canada. Genome Canada http://www.ch.embnet.org/software/SAPS_form.html Calculations include compositional analysis, charge distribution, identification of highly hydrophobic (transmembrane) segments, sequence repeats, and more. SAPS - Statistical Analysis of Protein Sequences http://140.120.213.10:8080/crsd/main/home.jsp Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS). CRSD http://scopes.biologie.hu-berlin.de/ MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights. MetaPath Online http://www.bioinfo.rpi.edu/applications/hybrid/ DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods. DINAMelt http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/ PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles. PRED-GPCR http://www.iipl.fudan.edu.cn/~lschen/kemadom.htm Kernal Machine for Domain Prediction (KemaDom) can predict the number of domains in a protein sequence using the local context information of neighboring amino acids. KemaDom http://www.nih.gov/science/models/mouse/resources/index.html Linked list of major mouse genome and mutation resources; maintained by the Trans-NIH Mouse Initiative. Mouse Resources http://theory.med.buffalo.edu/ Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/ analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/ analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA). Services from Zhou Laboratory http://invention.swmed.edu/etblast/etblast.shtml eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query. eTBLAST http://biit.cs.ut.ee/gprofiler/ g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. g:Profiler http://www.cisreg.ca/oPOSSUM_new/ oPOSSUM is a web-based system for the detection of over- represented transcription factor binding sites in the promoters of sets of genes. oPOSSUM http://ibivu.cs.vu.nl/programs/pralinewww/ Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction. PRALINE http://salilab.org/DBAli/ DBAli is a database that includes a comprehensive all- against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions. DBAli http://www.sagenet.org/ Serial Analysis of Gene Expression; simultaneous expression and map information. SAGE Home Page PERL http://repeats.abc.hu/cgi-bin/plotrep.pl PlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output. PlotRep http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families. SVM-PROT http://tlife.fudan.edu.cn/ltr_finder/ LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences. LTR_Finder http://baboon.math.berkeley.edu/mavid/ MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions. MAVID http://www.emolecules.com/index.htm eMolecules is a search engine for chemical structures that allows for substructure searching. eMolecules T-COFFEE http://www.tcoffee.org/ The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool that is more accurate than ClustalW for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments. M-Coffee is a meta- method for computing multiple sequence alignments by combining alternative alignment methods. http://regrna.mbc.nctu.edu.tw/ Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5'-UTR and 3'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites. RegRNA http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections. NCBI Bookshelf http://www.paralign.org/ ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment). ParAlign http://bioinfo.bsd.uchicago.edu/MutScreener.html MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations. MutScreener http://www.genome.jp/kegg/kaas/ KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways. KAAS http://www.ebi.ac.uk/microarray/MIAMExpress/miamexpress.html MIAME (minimum information about a microarray experiment) compliant microarray data submission tool. MIAMExpress http://espript.ibcp.fr/ESPript/ENDscript/index.php ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information. ENDscript http://pvsoar.bioengr.uic.edu/ pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure. pvSOAR http://kinasephos2.mbc.nctu.edu.tw/ KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool. KinasePhos 2.0 RNA http://ocw.mit.edu/ MIT OpenCourseWare provides free and open access to some of MIT's course materials. There are hundreds of courses represented from over thirty different disciplines, including Biology, Health Sciences and Technology, and Science, Technology, and Society. No registration is required. MIT OpenCourseWare http://bioinformatics.univ-reunion.fr/analycys/ AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering. AnalyCys http://www.intlgenome.org/viewDatabase.cfm The International Sequencing Consortium (ISC) Large- scale Sequencing Project Database contains information on current and completed sequencing projects, including project timelines, funding agencies, sequencing strategy and links out to project web pages. ISC Large-scale Sequencing Project Database Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools. http://cbcsrv.watson.ibm.com/Tspd.html IBM Bioinformatics and Pattern Discovery Group http://www.cbs.dtu.dk/services/VirtualRibosome/ The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/ exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results. Virtual Ribosome http://www.glycosciences.de/glyprot/ Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure. Glyprot http://wavis.img.cas.cz/ The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments. WAViS http://proteomics.mcw.edu/denovoid/ DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments. DeNovoID http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes. YMF 3.0 http://bioruby.org/ The BioRuby project aims to implement an integrated environment for bioinformatics with Ruby. BioRuby Model_Organisms http://genome.ucsc.edu/cgi-bin/hgGateway? org=Fugu&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the Fugu genome at any scale, together with dozens of aligned annotation tracks. UCSC Fugu Genome Browse Gateway https://fungalgenome.concordia.ca/tools/OrfPredictor.html OrfPredictor is designed for prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences. OrfPredictor http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms. TOUCAN 2 http://www.ebi.ac.uk/integr8/ Integr8 is a browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO. Intergr8 http://ibivu.cs.vu.nl/programs/popswww/ Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level. POPS http://spliceport.cs.umd.edu:2000/SplicingAnalyser2.html SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites. SplicePort http://www.sanger.ac.uk/Software/Rfam/ Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families. Rfam http://www.bioinformatics.ca/ Hands-on instruction in the use and development of software tools for genomic and computational biology research. Canadian Bioinformatics Workshops http://andromeda.gsf.de/arts ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels. ARTS http://foldminer.stanford.edu/ FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm. FoldMiner and LOCK 2 http://crispr.u-psud.fr/Server/CRISPRfinder.php Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea. CRISPRFinder http://structure.bu.edu/cgi-bin/consensus/consensus.cgi The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling. Consensus Server http://www.ee.surrey.ac.uk/Teaching/Unix/ Excellent tutorial for unix beginners. UNIX Tutorial for Beginners http://max.ucmp.umu.se/sahmm/ Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains. FISH http://bioportal.weizmann.ac.il/promate/ ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations. ProMateus http://www.ensembl.org/info/software/index.html Ensembl is a freely available software system for genomic analysis. The documentation page at Ensembl is the best place to get information on the Ensembl application programming interface (API). In particular, the tutorial document includes lots of examples of scripts and exercises for you to try. Ensembl API http://dis.embl.de/ A computational tool for prediction of disordered/ unstructured regions within a protein sequence. DisEMBL http://www.chilibot.net/ Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph. Chilibot http://www.ebi.ac.uk/Tools/webservices/ EBI Tools EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. http://www.ebi.ac.uk/Wise2/promoterwise.html Compares two DNA sequences allowing for inversions and translocations, ideal for promoters. PromoterWise Localization_and_Targeting Protein_Expression http://evolution.genetics.washington.edu/phylip.html Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX. PHYLIP http://biodas.org/ This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data. BioDAS http://www.ensembl.org/Caenorhabditis_elegans/ Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl's comparative genomics resources. Ensembl C.elegans Genome Browser Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure "meta"-tools as a pipeline of individual tools and intermediate filters. MIGenAS Toolkit http://www.migenas.org/ http://tstag.molgen.mpg.de/ Tissue-Specific Transcripts And Genes (T-STAG) is a system integrating EST, gene expression, alternative splicing and human-mouse orthology information for the analysis of tissue-specific gene and transcript expression patterns. T-STAG Function http://smi-web.stanford.edu/projects/helix/sstructview/ RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends. SStructView http://fatcat.burnham.org/ FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm. FATCAT http://ms.iis.sinica.edu.tw/Multi-Q-Web/ Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling. Multi-Q http://indelscan.genomics.sinica.edu.tw/IndelScan/ INDELSCAN is a tool for genome-wide identification of indels. INDELSCAN http://www.sbml.org/ The Systems Biology Markup Language (SBML) is a computer- readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology. Systems Biology Markup Language (SBML) http://www.icgeb.org/protein/ ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models. ICGEBnet Protein Tools http://bioinformatics.ubc.ca/resources/tutorials/ A collection of bioinformatics tutorials developed at the UBC Bioinformatics Centre. The tutorial subject matter ranges from using tools such as BLAST and ClustalX to more general computing matters like installing Cygwin and using the UNIX operating system. UBiC Tutorials http://www.maizegdb.org/ A central repository for public maize information. Maize Genetics and Genomics Database http://ceas.cbi.pku.edu.cn Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs. CEAS http://www.sfu.ca/~ibajic/NXSensor/ Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function. NXSensor http://www.povray.org/ Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication. POV-Ray Databases http://evolution.genetics.washington.edu/phylip/software.html Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip. Joes Site - Phylogeny Programs http://bioinformatics.weizmann.ac.il/~milana/OneCYRCA/ One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods. One-Block CYRCA http://bioinformatics.albany.edu/~mitopred/ MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers. MITOPRED http://mml.sjtu.edu.cn/MobilomeFINDER/ MobilomeFINDER (Mobile Genome FINDER) is a tool for high- throughput genomic island discovery. MobilomeFINDER http://disulfind.dsi.unifi.it/ DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence. DISULFIND http://snp.cshl.org/ Non-profit foundation whose mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make this information available to the public without intellectual property restrictions. The SNP Consortium PANTHER Tools http://www.pantherdb.org/tools/ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data. http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation. RNAz http://bio.cs.washington.edu/MicroFootPrinter.html MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter. MicroFootPrinter http://genealign.hccvs.hc.edu.tw/index.htm GeneAlign is a gene prediction tool that uses conservation of gene structures and sequence homologies between protein coding regions to increase prediction accuracy. GeneAlign is currently configured to align human and mouse sequences for gene prediction. GeneAlign http://protinfo.compbio.washington.edu/ Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling. Protinfo http://synor.dcode.org/ SynoR searches vertebrate genomes for synonymous regulatory elements. SynoR http://www.tigr.org/tdb/mdb/mdbcomplete.html Table of complete and in-progress microbial genomes with links to publications. TIGR Microbial Database http://3motif.stanford.edu/ 3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files. 3Motif Mouse_and_Rat http://lagan.stanford.edu/lagan_web/index.shtml The LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment program), Multi-LAGAN , and Shuffle-LAGAN (both variations of LAGAN). LAGAN http://atgc.lirmm.fr/phyml/ Phyml is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. PHYML http://okeylabimac.med.utoronto.ca/PUNS/ The Primer-UniGene Selectivity Testing software system (PUNS) assists in the specificity design of PCR primers. A set of primers must be physically designed first. Then PUNS can be used to estimate the expected number of different amplification products using NCBI's UniGene database as representative of species transcriptomes. PUNS: Primer-UniGene Selectivity Testing http://www.ebi.ac.uk/interpro/index.html Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches. InterPro http://bioinformatics.bc.edu/clotelab/DIAL/ DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA. DIAL http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment. Cn3D http://www.mouseatlas.org/ A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries. Mouse Atlas of Gene Expression http://consurf.tau.ac.il/ The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf http://genie.dartmouth.edu/scope/ SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE http://pda.uab.es/pda2/ PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database. PDA Java http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html The Human Gene Mutation Database comprises various types of mutation within the coding regions of human nuclear genes causing inherited disease. Human Gene Mutation Database http://probalign.njit.edu/probalign/login eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output. eProbalign Microbes http://tools.neb.com/NEBcutter/index.php3 NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb. NEBcutter http://sride.enzim.hu/ Sride is a tool for identificating stabilizing residues in protein structure. Sride http://www.snubi.org/software/ArrayXPath/ ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams. ArrayXPath http://mammoth.bcm.tmc.edu/report_maker/ Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins. ET Report Maker http://www.softberry.com/berry.phtml? topic=promhg&group=programs&subgroup=promoter PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences. PromH http://www.cbs.dtu.dk/services/FeatureExtract/ The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files. FeatureExtract http://www.bioinfotool.org/domac.html DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together. DOMAC http://www.yasara.org/ YASARA (Yet Another Scientific Artificial Reality Application) is a software package for visualization, simulation and modeling of molecules. It uses Portable Vector Language (PVL) which allows the visualization of very large proteins. YASARA View is available for free, and is primarily a visualization tool. YASARA http://eclair.btk.fi/ Eclair is a web service that implements the Eclat (EST CLAssification Tool) support vector machine (SVM) approach for the classification of species origin for, primarily, expressed sequence tags (ESTs) Eclair http://www-rcf.usc.edu/~forsburg/bio.html Provides a starting point for biologists who are women; includes information on the history of women in science, education of women scientists, organizations, and careers. Women in Biology Internet Launch Pages 3-D_Structural_Features http://gepas.bioinfo.cipf.es/ The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. GEPAS http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/ Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces. I2I-SiteEngine http://www.tree-puzzle.de/ Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. TREE-PUZZLE http://www.biophp.org/ Open Source PHP code for bioinformatics. Includes functions and minitools (copy and paste one page scripts for basic tasks in bioinformatics. A wiki-like service allows modification and improvement of code. BioPHP https://catalog.invitrogen.com/index.cfm? fuseaction=userGroup.home VectorNTI is an application for integrated for molecular sequence analysis including primer design, virtual cloning, alignments, and sequence assembly. The free license needs to be renewed every year. VectorNTI http://string.embl-heidelberg.de:8080/prophecies_html/ prophecies.html ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes. ArrayProspector http://discover.nci.nih.gov/matchminer/ MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references. MatchMiner http://caps.ncbs.res.in/DIAL/home.html DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein. DIAL http://prowl.rockefeller.edu/ Software tools and integrated databases to facilitate analyzing the output from protein mass spectrometry experiments. PROWL http://cbit.snu.ac.kr/~ProMiR2/ Probabilistic miRNA prediction (ProMiR) is a resource that includes: ProMiR-v to search for both conserved and non- conserved miRNAs in the vicinity of a known miRNA; ProMiR-c to predict both conserved and non-conserved miRNAs in the vicinity of a candidate (70~150 nt); and ProMiR-g to predict miRNA genes in a long sequence (70 nt~10 kb) of various speceis. ProMiR II http://www.jvirgel.de/ JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes. JVirGel http://www.jbirc.aist.go.jp/tact/ Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H- Inv) project. TACT http://www.ibt.unam.mx/biocomputo/RibEx.html Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved RibEx http://fugu.hgmp.mrc.ac.uk/ Comparative mapping and sequencing to facilitate human genome annotation. HGMP-RC Fugu Genome Project http://sage.csb.yale.edu/sitefinder3d/ SiteFINDER|3D predicts functionally important regions in proteins of known structure using conserved functional group (CFG) analysis. SiteFINDER|3D http://www.procksi.net/ ProCKSi (Protein Comparison using Kolmogorov and other Similarity Measures) is a multi-layer protein comparison meta-server that computes structure similarities using information theory measures. ProCKSi http://www.genome.gov/PolicyEthics/ Critical issues and legislation surrounding genetic research. Hosted by the National Human Genome Resarch Institute (NHGRI). NHGRI Policy and Ethics http://www.vanbug.org Association of researchers, other professionals, and students in the BC Lower Mainland who have an interest in bioinformatics; monthly meetings will be held to present work, ask questions, share tips and tricks. VanBUG - Vancouver Bioinformatics User Group http://www.bcgsc.ca/lab/mapping/mouse BAC fingerprint map of the mouse genome, completed by Genome Sciences Centre, Vancouver. Mouse BAC Physical Map http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp CPC (Coding Potential Calculator) distinguishes protein- coding from non-coding RNAs based on the sequence features of the input transcripts. CPC http://mips.gsf.de/ Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT. MIPS http://www.bioinfo.no/tools/bomp The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram- negative bacteria as input and predicts whether or not they are beta- barrel integral outer membrane proteins. BOMP http://www.ebi.ac.uk/2can/ The site contains tutorials, a glossary, and introductory articles on various topics related to bioinformatics and molecular and cell biology. The emphasis is on an increased understanding of the databases and tools available from the European Bioinformatics Institute (EBI) and its collaborators. 2can Bioinformatics Educational Resource http://bioinfo.curie.fr/CAPweb/ CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data. CAPweb https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/ The BRIDGE-based Genome-Transcriptome-Proteome Browser (BRIGEP) comprises three open-source web-based systems: GenDB, ProDB and EMMA. GenDB is a bacterial genome annotation system, ProDB is a storage and analysis system for mass spectrometry data, and EMMA is a storage and analysis system for transcriptome data. BRIGEP http://genomes.urv.es/OPTIMIZER/ OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems. OPTIMIZER http://www.ncbi.nlm.nih.gov/COG/ Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest. COGs http://bioserv.rpbs.jussieu.fr/cgi-bin/SCit SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/ or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure. SCit http://www.ebi.ac.uk/expressionprofiler/ Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data. Expression Profiler http://www.ebi.ac.uk/newt/display NEWT is the taxonomy database maintained by the UniProt group. NEWT http://www.bioinfo.biocenter.helsinki.fi/poxo POXO is a series of tools that can be used to discover, search, and verify transcription factor binding sites (TFBS) from sets of co-expressed genes. POXO http://cluster.physics.iisc.ernet.in/ssep/options.html Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB. SSEP http://www.tigr.org/software/ A list of open-source software packages available for free from The Institute for Genomic Research (TIGR). TIGR Software Tools http://bibiserv.techfak.uni-bielefeld.de/agenda/ AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence. AGenDA http://feature.stanford.edu/webfeature/ WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures. WebFEATURE http://www.ihop-net.org/UniPub/iHOP/ iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model. iHOP http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules. Assembly PCR Oligo Maker http://biopipe.org/ The biopipe is a workflow framework that seeks to address some of the complexity involved in carrying out large scale bioinformatics analysis. It has been designed to work intimately with the bioperl package. BioPipe http://as2ts.llnl.gov/AS2TS/LGA/lga.html Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures. LGA http://protein.bio.puc.cl/cardex/servers/sagexplore/home.php SAGExplore is a tool for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). SAGExplore http://us.expasy.org/swiss-shop/ Submit sequence, pattern or keywords to receive email alert when new sequences of interest appear in SwissProt. Swiss-Shop http://biominer.bime.ntu.edu.tw/ipda/ iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence. iPDA http://www.esil.univ-mrs.fr/~dgaut/download/ RNA motif search program; not a Web-tool. RNAMOT http://sivirus.rnai.jp/ siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference. siVirus http://us.expasy.org/tools/protparam.html Compute molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. ProtParam http://seqhound.blueprint.org/ Seqhound is a sequence retrieval system that provides access to biological sequence, structure and functional annotation data. Seqhound can be accessed via the web interface, through the remote API, or by installing locally. SeqHound http://corgen.molgen.mpg.de CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters. CorGen http://www.genetics.wustl.edu/eddy/software/#rnabob Fast RNA motif/pattern searcher; from the authors: If you re looking for an RNA motif that fits a hard consensus pattern -- a la PROSITE patterns, but with base-pairing -- you might check out RNABOB; not a Web-tool; based on RNAMOT. RNABOB http://egassembler.hgc.jp EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing. EGassembler http://www4.rothamsted.bbsrc.ac.uk/whets/cgi-bin/whets1.2/ whets_home.pl WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design. WhETS http://www.ncbi.nlm.nih.gov/genome/seq/ Downloadable human DNA reference sequence. Annotation of genes and other genomic features will be available for browsing when complete. NCBI Human DNA Reference Sequence http://string.embl.de/ STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a protein-protein interaction/association database. Both known and predicted interactions are included. The interactions are derived from existing data sources and literature and from high-throughput experiments. Predictions are also made based on an analysis of genomic context. STRING http://www.gene-regulation.com/pub/databases.html includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database. BIOBASE Gene Regulation databases http://www.russell.embl.de/pints/ Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities. PINTS http://genome-www.stanford.edu/Saccharomyces/ The Saccharomyces Genome Database. SGD http://www.tigr.org/tdb/GeneSplicer/ A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice. GeneSplicer http://www.ncbi.nlm.nih.gov/gorf/gorf.html Finds all open reading frames in a sequence. ORF Finder http://www.ncbi.nlm.nih.gov/Taxonomy Taxonomic classification of all organisms with sequences in GenBank. NCBI Taxonomy Database http://scor.berkeley.edu/ The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships. SCOR http://lowelab.ucsc.edu/tRNAscan-SE/ tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC) tRNAscan-SE http://sirw.embl.de/ SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/ nucleotide databases with keywords and a sequence motif. SIRW http://www.SNPbox.org Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server. SNPbox Tools_For_the_Bench http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses. GeMprospector Gene_Regulation http://3dlogo.uniroma2.it/3dLOGO/home.html 3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures. 3dLOGO http://snowdeal.org/section/informatics/ A weblog that provides daily updates and links to news items and stories of interest to bioinformatics community. snowdeal.org > {bio,medical}informatics http://genome.cs.mcgill.ca/cgi-bin/FootPrinter3.0/ FootPrinterInput2.pl FootPrinter3 is a web server for predicting transcription factor binding sites (TFBS) by using phylogenetic footprinting. FootPrinter3 extends the motif discovery algorithms of FootPrinter by making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions. FootPrinter3 http://java.sun.com/docs/books/tutorial/ The place to go for your first cup of Java. The Java Tutorial http://www.genelynx.org A portal to the human genome. Query by text or BLAST, to access heaps of info from primary and secondary databases of genomic resources, transcripts, protein sequences, function, associated diseases, homologs, ests. GeneLynx http://genstyle.imed.jussieu.fr/ GENSTYLE is based on the genomic signature paradigm and allows the user to classify and characterize nucleotide sequences using oligonucleotide frequencies. GENSTYLE http://interviewer.inha.ac.kr/ WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly. WebInterViewer http://bioweb.pasteur.fr/seqanal/interfaces/cap3.html Web-based contig assembly. CAP3 Sequence Assembly Program http://algorithm.cs.nthu.edu.tw/tools/SPRING Sorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results. SPRING http://www.sysbiosociety.ca:8200/ The Canadian Society for Systems Biology aims at supporting and developing initiatives that strengthen Systems Biology research in Canada. Canadian Society for Systems Biology http://www.genomeweb.com/ News reports on the business and technology of genomics, updated continuously throughout the business day. Genome Web http://www.genome.arizona.edu/software/fpc/ FPC is a tool to assemble contigs from a set of clones and their restriction fragments. FPC http://msa.cgb.ki.se/cgi-bin/msa.cgi Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality. Kalign, Kalignvu, and Mumsa http://www.ncbi.nlm.nih.gov/Tour/ Introduction to how the draft sequence of the human genome can be used by biologists, includes examples of the types of questions that can be answered with the data. How to Use the Human Draft Sequence http://ekhidna.biocenter.helsinki.fi/pobo A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation. POBO http://www.imtech.res.in/raghava/algpred/ AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches. AlgPred http://idconverter.bioinfo.cnio.es/IDconverter.php IDconverter is a tool that converts gene, clone or protein IDs to other IDs which can be especially useful for microarray data analyses. This application is part of the suite Asterias. IDconverter http://darwin.nmsu.edu/cgi-bin/graph_align.cgi Provides graphical representations of ClustalW global pairwise alignments for query and subject sequences from BLAST type searches. Graphical representation provides information on high quality sections of the global alignment. GraphAlign Analysis_of_Aligned_Sequences http://botdb.abcc.ncifcrf.gov/ botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either 'botulinum' or 'tetanus' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB. botXminer http://www.cs.ualberta.ca/~bioinfo/PA/ Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi- blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User- supplied training data can also be used to create custom classifiers. Proteome Analyst http://hum-molgen.org/ The HUMan MOLecular GENetics Portal Site (HUM-MOLGEN) is a source of various types of information related to human molecular genetics, including: news, lists of and links to biomedical companies and journals, job and event listings and discussion forums. HUMan MOLecular GENetics Portal Site http://www.nii.res.in/nrps-pks.html NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products. NRPS-PKS http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp QPPD (Quantitative PCR Primer Database) contains information about primer sets published for quantitative PCR assays. This database can be searched by gene name, keyword, or by identifier. Results return primer sequences, graphics showing the primer location, and PubMed ID for the original reference. QPPD http://www.pdg.cnb.uam.es/Servers/treedet/ Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments. TreeDet Microarrays http://biowulf.bu.edu/zlab/PromoSer/ Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site. PromoSer http://ndbserver.rutgers.edu/services/ The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures. NDB Tools http://www.doe-mbi.ucla.edu/Services/GDAP The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes. GDAP http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi? The NCBI Map Viewer provides graphical displays of features on NCBI's assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps. NCBI Map Viewer http://prodata.swmed.edu/promals/promals.php PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI- BLAST searches and secondary structure predictions from PSIPRED. PROMALS CBS DAS protein viewer The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence. http://www.cbs.dtu.dk/cgi-bin/das http://www.infoway-inforoute.ca/en/home/home.aspx Canada Health Infoway is working to develop a network of electronic health records across Canada in order to improve the quality and access to healthcare services, therefore making them more productive. Canada Health Infoway http://stat.genopole.cnrs.fr/spatt/index.html Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences. SPatt http://www.ensembl.org/Rattus_norvegicus/ The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus). Ensembl Rat Genome Browser http://www.genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first. Primer3 http://us.expasy.org/ch2d/2d-index.html References to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services. ExPASy 2-D PAGE databases and services http://brop.org/ The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database. BROP http://cpndb.cbr.nrc.ca/home.php cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools. cpnDB http://datf.cbi.pku.edu.cn The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis. DATF http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/ Clustal X is a version of the Clustal W multiple sequence alignment program with a graphical interface. The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris. ClustalX Carbohydrates http://www.bioinf.seu.edu.cn/miRNA/ miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors. miPred http://www.sysbio.muohio.edu/CodonO/ CodonO is a method for measuring synonymous codon usage bias within and across genomes. CodonO PHP http://iubio.bio.indiana.edu:8089/ Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information. euGenes: Genomic Information for Eukaryotic Organisms http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/ RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence. RNA Analyzer http://zeldia.cap.ed.ac.uk/nematodeESTs/nembase.html NEMBASE2 is a database resource for EST datasets for 37 species of nematode. Sequences are clustered to redunce redundacy. Comparisons can be by library and at a sequence level; a visualisation tool is included. Coding region predictions for each cluster, further annotations such as GO terms and physical properties are also included. NEMBASE2 http://www.gene.ucl.ac.uk/nomenclature/ The HGNC approves a unique gene name and symbol for each known human gene. The Human Gene Nomenclature Database (Genew) is searchable, and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous symbols and links out to sequence data. HGNC: HUGO Gene Nomenclature Committee http://crick.mbu.iisc.ernet.in/~PIC/ Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex. PIC http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/ BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data. BioBayesNet http://cubic.bioc.columbia.edu/services/uniqueprot/ UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine. UniqueProt http://us.expasy.org/sprot/ Swiss-Prot is a curated database of protein sequences that are highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to Swiss-Prot, containing computer-annotated translations of EMBL sequences. Swiss-Prot and TrEMBL http://gfs.unc.edu/cgi-bin/WebObjects/GFSWeb Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived. GFS http://flybase.bio.indiana.edu/ FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster. FlyBase http://www.wormbase.org/ Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae. WormBase http://www.r-project.org/ System for statistical computation and graphics; an interpreted computer language which allows branching and looping as well as modular programming using functions. R http://www.ucmp.berkeley.edu/exhibit/phylogeny.html "Phylogeny-Diversity of Life Through Time" is an on-line exhibit at the University of California Museum of Paleontology website. There is an introduction to phylogenetics and cladistics, and you can navigate through a very informative phylogenetic tree rooted at the three main domains of life (Archaea, Bacteria and Eukaryota). At each level of the tree there is a brief summary, and links to more information about the Fossil Record, Life History and Ecology, Systematics and Morphology. UCMP Phylogeny Wing http://sky.bsd.uchicago.edu/DNannotator.htm DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user- defined annotations onto different versions of genomic sequences (< 30Kb size limit). DNannotator http://kinasephos.mbc.nctu.edu.tw/ KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences. KinasePhos http://wishart.biology.ualberta.ca/SuperPose/ SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules. SuperPose http://sfold.wadsworth.org Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features. Sfold http://pbil.univ-lyon1.fr/software/seaview.html SeaView is a graphical multiple sequence alignment editor that is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment. Seaview http://www.genetics.wustl.edu/eddy/software/#pk Predict pseudoknot structures in RNA sequence; source code only. PKNOTS http://www.cbio.mskcc.org/prl/index.php The Pathway Resource List (PRL) is a database of 150+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams, protein sequences, and protein-compound interactions. Pathway Resource List http://watcut.uwaterloo.ca/watcut/template.php WatCut allows you to perform restriction analysis and silent mutation analysis. The restriction analysis results can be displayed as a table or graphically to compare the results of different digests. All commercially available type II restriction enzymes are known. The silent mutation analysis scans your oligonucleotide sequence for restriction sites that could be introduced without altering the protein that is encoded. WatCut http://localizome.org/ Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information. Localizome http://ccb.imb.uq.edu.au/svmtm/svmtm_predictor.shtml Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format. SVMtm http://www.biocarta.com/ Information about gene function, proteomic pathways, and reagent exchange; very clear pathway diagrams; can search for pathways by title or browse an organized list. BioCarta http://bioinfo3d.cs.tau.ac.il/SymmDock/ SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking. SymmDock http://tubic.tju.edu.cn/GC-Profile/ GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. GC-Profile http://antigen.i2r.a-star.edu.sg/predBalbc/ PredBALB/c is a tool that will predict MHC binding peptides in your protein sequence of interest for the H2d haplotype of the BALB/c mouse. PredBALB/c http://power.nhri.org.tw/ The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences. POWER http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam). Cascade PSI-Blast http://schubert.bio.uniroma1.it/CAMPO/index.html CAMPO is a tool to analyze conserved regions from a multiple sequence alignment CAMPO http://bioinfo.pl/Meta/ 3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach. 3D-Jury http://bioinfo3d.cs.tau.ac.il/PatchDock/ PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria. PatchDock Interactions__Pathways__Enzymes http://www.matrixscience.com/ Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases. MASCOT (Matrix Science) http://pcons.net/ Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach. Pcons.net http://www.biojava.org/ The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. BioJava http://www.chr7.org/ The Chromosome 7 database is a community-curated project which contains the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. The Chromosome 7 Annotation Project http://bibiserv.techfak.uni-bielefeld.de/genefisher/ Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences. Genefisher http://btweb.aua.gr:8080/crystwiv/ CrysTwiV (Crystal Twin Variables) is an automated approach for phase extension and refinement in X-ray crystallography; free registration is required for use. CrysTwiV http://robotics.stanford.edu/~xsliu/BioProspector/ Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations. BioProspector http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other. SiteEngine http://sledgehmmer.sdsc.edu/ SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail. SledgeHMMER http://www.chem.cuhk.edu.hk/DSHIFT/ DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form. DSHIFT http://www.bind.ca/ Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records. BIND - The Biomolecular Interaction Network Database http://www.t10.lanl.gov/billb/weighbor/index.html Weighbor is a tool for building phylogenetic trees from distance matrices. It employs a weighted version of the neighbour- joining method in which longer distances in the matrix are given less weight. Weighbor http://genome.ucsc.edu/cgi-bin/hgGateway?org=C. +elegans&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the C. elegans genome at any scale, together with dozens of aligned annotation tracks. UCSC C. elegans Genome Browser Gateway http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/ server.html RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis. Riboswitch finder http://www.imtech.res.in/raghava/gpcrsclass/ GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user. GPCRsclass http://lorentz.immstr.pasteur.fr/joel/index.php MinActionPath calculates the most-probable trajectory between two known structural states of a protein. MinActionPath http://bioinfo.thep.lu.se/acid.html The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly. ACID Similarity_Searching http://www.biostat.harvard.edu/complab/gosurfer/ GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wide computations. GoSurfer http://lorentz.immstr.pasteur.fr/solvate_mutate.php PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones. PDB_Hydro http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.html Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM). MeMo http://www.cbs.dtu.dk/services/RNAmmer/ RNAmmer predicts genes for ribosomal RNA (rRNA) in full genome sequences using hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. RNAmmer Bioinformatics A bioinformatics web resource http://bioinfo.unice.fr/biodiv/Tree_editors.html Tree Editors is an annotated listing of software for the visualization and manipulation of phylogenetic trees. Tree Editors Metabolites 3-D_Structure_Retrieval__Viewing http://ndbserver.rutgers.edu/ NDB (Nucleic Acid Database) is a repository of three- dimensional structural information about nucleic acids. NDB http://melina2.hgc.jp/public/index.html MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions. MelinaII http://www.affymetrix.com/analysis/index.affx Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required. Affymetrix NetAffx Analysis Center Yeast http://www.tigr.org/tdb/bac_ends/mouse/bac_end_intro.html TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; BACs are same as those fingerprinted by Genome Sciences Centre, Vancouver. Mouse BAC Ends http://design.RNAi.jp/ Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates. siDirect http://www.geneclinics.org/ GeneTests is a medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons GeneTests http://wishart.biology.ualberta.ca/shiftor/cgi-bin/ preditor_current.py PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions. PREDITOR http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). CATH http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database. CMR http://globplot.embl.de/ GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction. GlobPlot http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/ w2h.open/w2h.startthis?SIMGO=w2h.welcome Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). OpenHUSAR http://www.phenomicdb.de/ PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison. PhenomicDB http://www.geneontology.org/ Organized, controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products in many organisms. Gene Ontology (GO) Consortium http://www.ergito.com/toc.jsp?bcs=EXP Short essays explaining classic experiments of the 20th century; most are written by one of the people who actually performed the experiments; free with registration. Great Experiments http://vakser.bioinformatics.ku.edu/resources/gramm/grammx GRAMM-X is a protein docking server. GRAMM-X http://www.ncbi.nlm.nih.gov/dbEST/index.html Expressed Sequence Tags database; a division of GenBank containing single-pass cDNA sequence reads dbEST http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies. SNPserver http://darwin.uvigo.es/software/modeltest_server.html ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses. ModelTest Sever http://www.ebi.ac.uk/biomart/ BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl). BioMart http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods. ProFunc http://e-rnai.dkfz.de/ E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in Drosophila and C. elegans; can also be used for the design of enzymatically-digested long dsRNA (esiRNAs) for mammalian cells. E-RNAi http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php CytoSVM is a Support Vector Machine (SVM) based server that predicts putative cytokine-receptor interactions based on a primary protein sequence. Using this method, results from screening the human and mouse genomes are available via a database search. CytoSVM http://bioinformatics.biol.rug.nl/websoftware/bagel/ bagel_start.php BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity. BAGEL http://bioinformatics.albany.edu/~ptarget pTARGET predicts the subcellular localization of eukaryotic proteins based on the occurrence patterns of location- specific protein functional domains and the amino acid compositional differences in proteins from nine distinct subcellular locations. pTARGET http://www.dsl.org/cookbook/ Tips and techniques for everyday use. The Linux Cookbook http://jura.wi.mit.edu/bioc/siRNA Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA. siRNA Selection Server http://www.xml.nig.ac.jp/index.html XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs. XML Central of DDBJ http://www.ncbi.nlm.nih.gov/Entrez/index.html NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed. Entrez http://www.ncbi.nlm.nih.gov/entrez/query/static/ eutils_help.html The Entrez Programming Utilities provide a method of linking to Entrez and querying the Entrez database outside of the regular web interface. Users can access the utilities via a web address, or via a Simple Object Access Protocol (SOAP) interface. Entrez Programming Utilities http://www.ebi.ac.uk/MPsrch Uses the Smith-Waterman algorithm; runs at BLAST-like speeds without losing sensitivity. MPSRCH http://acmes.rnet.missouri.edu/ ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches. ACMES http://locate.imb.uq.edu.au/ LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins. LOCATE http://www.proteios.org/ Proteios is an initiative to create an open-source storage, analysis and organization system for proteomics experiments. Proteios - The Open Source Proteomics Initiative http://pedrodownload.man.ac.uk/ Software and schemata for modelling, capturing and disseminating proteomics experimental data PEDRo http://phylogeny.arizona.edu/ Multi-authored project attempting to represent online the entire phylogeny of life on earth. Tree of Life Do-it-all_Tools_for_Protein Other_Organisms http://www.nslij-genetics.org/bioinfotraining/ A list of programs, workshops and individual courses in bioinformatics maintained at the Robert S. Boas Center for Genomics and Human Genetics. A List of Bioinformatics Courses Molecular_Dynamics_and_Docking Linux-Unix http://brak.sdsc.edu/pub/BiologicalNetworks/ BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps. BiologicalNetworks http://www.ensembl.org/Fugu_rubripes/ Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome. Ensembl Fugu Genome Browser http://pubcrawler.gen.tcd.ie/ It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes). PubCrawler http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/ WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication. WEB-THERMODYN http://perl.com The homepage of the perl programming language. Perl.com http://gels.ethics.ubc.ca/links.htm Ethical issues in genomics from Genomics, Ethics, Environment, Economics, Law, and Society (GE3LS). Democracy, Ethics and Genomics http://www.genome.clemson.edu/gdr/ Genome Database for Rosaceae (GDR) contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map. Genome Database for Rosaceae http://phobius.cgb.ki.se/ Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions. Phobius http://www.bioteach.ubc.ca/ Great articles on all sorts of biological topics including bioinformatics. BioTeach http://csb.stanford.edu/~nbatada/VCN.html CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered. CNplot: Visualization of Pre-Clustered networks http://genome.ucsc.edu/cgi-bin/hgGateway? org=Mouse&db=0&hgsid=27736277 Provides a rapid and reliable display of any requested portion of the mouse genome at any scale, together with dozens of aligned annotation tracks. UCSC Mouse Genome Browser Gateway Ethics http://www.methdb.de/ The database contains information about the occurrence of methylated cytosines in the DNA. DNA Methylation Database http://www.genome.gov/glossary.cfm Includes audio explanations of terms by researchers in the relevant field of study; Francis Collins explains shotgun sequencing. Glossary of Genetic Terms, NHGRI https://pathwayexplorer.genome.tugraz.at/ Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP. Pathway Explorer http://www.bioinformatics.nl/cgi-bin/primer3plus/ primer3plus.cgi Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program. Primer3Plus http://www.imtech.res.in/raghava/pcleavage/ Pcleavage is a tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences. Pcleavage http://www.bioneq.qc.ca/ A network to coordinate Bioinformatics activities in Quebec. BioneQ http://searchlauncher.bcm.tmc.edu/ Molecular biology-related search and analysis services organized by function; single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters). BCM Search Launcher http://www.rcsb.org/pdb/Welcome.do Protein Data Bank; includes theoretical structures. PDB http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v35/ n1s/index.html Hands-on tutorial for using genome browsers as web tools for browsing and analyzing data from the Human Genome Project and other sequencing efforts; features UCSC Genome Browser, NCBIs Map Viewer, and Ensembl Genome Browser. Users Guide to the Human Genome http://www.secretomes.umn.edu/AMOD/ AMOD (Assisted Morpholino Design) is a tool for designing antisense morpholino oligonucleotides (reagents to modulate gene expression) for an input sequence. AMOD http://cubic.bioc.columbia.edu/services/nlprot/index.html NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases. NLProt http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html Simple Sequence Repeats (SSR) Primer aids in design of primers that can amplify microsatellite sequences. SPUTNIK is used to screen for SSR and Primer3 for locus specific primer design. Precomputed results can be viewed using the SSR Taxonomy Browser. SSR Primer http://prodata.swmed.edu/compass/compass.php COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. COMPASS http://www.gene-regulation.com/pub/programs/cma/CMA.html Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes. CMA http://www-ab.informatik.uni-tuebingen.de/software/crosslink/ webstart/welcome.html Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets. CrossLink http://pipeline.lbl.gov/cgi-bin/gateway2 The Berkeley Genome Pipeline a.k.a. Godzilla, provides precomputed VISTA plots of sequence conservation between pairs of human, mouse or rat genomes. Godzilla http://foldalign.kvl.dk/ FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences. FOLDALIGN http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment. SA-Search http://zeus.cs.vu.nl/programs/seqharm/ Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings. Sequence Harmony http://biodata.mshri.on.ca/grid Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically. The GRID - General Repository for Interaction Datasets http://imex.sourceforge.net/ The IMEx consortium is a group of major public interaction data providers intending to share curation effort and exchange completed records on molecular interaction data, similar to successful global collaborations for protein and DNA sequences and for macromolecular structures. IMEx http://bioinfo.cnio.es/cargo/cargo.html CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human. CARGO http://www.isrec.isb-sib.ch/ssa/ Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site). SSA http://mesquiteproject.org/mesquite/mesquite.html Mesquite is an open source software project designed to deal with comparative data about organisms and evolutionary analyses. Mesquite contains modules for phylogenetic analysis, population genetics, and non-phylogenetic multivariate analysis. Mesquite http://trafac.cchmc.org/trafac/index.jsp TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach. TraFaC http://bussemaker.bio.columbia.edu/reduce/ REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required. REDUCE http://cbm.bio.uniroma2.it/SH3-Hunter/ SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences. SH3-Hunter http://www.cbs.dtu.dk/services/RevTrans/ RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment. RevTrans http://www.ensembl.org/ Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes. Ensembl Genome Browser http://muscle.cribi.unipd.it:2701/ MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data. MIDAW http://trantor.bioc.columbia.edu/SMS/JPD/ Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for structurally aligned pairs of PDB files. JPD Worm http://darwin.uvigo.es/software/gendecoder.html GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon- usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence. GenDecoder Motifs http://www.genome.ad.jp/kegg/ Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG: Kyoto Encyclopedia of Genes and Genomes http://bioinfo.lifl.fr/yass/ YASS performs local alignments of DNA sequences. It is available through a web interface and as a standalone command-line tool. YASS http://www.cisred.org/ cisRED is a database system for genome-scale computational discovery of regulatory elements. cisRED http://treg.molgen.mpg.de/ T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar). T-Reg Comparator http://rgd.mcw.edu/ The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis. Rat Genome Database (RGD) http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules. oGNM http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/ Great tutorial for those interested in the bioperl group of modules. BioPerl course http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi Predict RNA secondary structure from sequence; note sequence length limit. RNAfold http://quasimotifinder.tau.ac.il/ QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs). QuasiMotiFinder http://genes.mit.edu/McPromoter.html The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites. McPromoter http://www.ensembl.org/Danio_rerio/ This ensembl website features the zebrafish whole genome shotgun assembly sequence. Ensembl Zebrafish Genome Browser http://bioinformatics.leeds.ac.uk/shark/ Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet. metaSHARK http://qscop-blast.services.came.sbg.ac.at/ QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins). QSCOP - BLAST http://www.biosci.ki.se/groups/tbu/logobar/ LogoBar is a Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments that show the amino acid incidence at every position. LogoBar http://www.s-star.org Aims to provide a bioinformatics education to interested students everywhere, regardless of background, with the help of the Internet. The lectures are also accessible to the public for those who do not wish to register in the courses. S-Star.org http://www.pht.uni-koeln.de Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite. Pathway Hunter Tool http://opaas.ibms.sinica.edu.tw/ Optimal, Permuted, and Other Alternative Alignments of Protein Structures (OPAAS) is a tool for investigating structural neighbors that can calculate a structural alignment for two protein structures. OPAAS http://genomebiology.com/drosophila/ A series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies. Genome Biology Release 3 of the Drosophila genome http://metnetdb.gdcb.iastate.edu/medkit/ MedKit is a helper application for text-mining the MEDLINE abstract database that allows allows random sampling of abstracts and downloads of >10,000 MEDLINE abstracts in XML form. Java modules (query, sample, fetch, and parse) that can be easily integrated into other text-mining systems are also included. MedKit http://lawgenecentre.org/ Contains numerous articles concerning the legal and ethical issues arising from the developments in genetic technology. Center for Law and Genetics http://www.imb-jena.de/RNA.html An RNA resource hub. The RNA World http://www.ornl.gov/sci/techresources/Human_Genome/elsi/ elsi.shtml Addresses a variety of ethical issues including genetic testing, gene therapy, privacy and patenting. Ethical, Legal, and Social Issues - Genome Research http://espript.ibcp.fr/ESPript/ESPript/index.php Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information. ESPript http://dasdfasdf.com 5&apos; lll test http://genome.jgi-psf.org/ The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt. DOE Joint Genome Institute Genome Portal Comparative_Genomics http://www.dcode.org/ The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser. DCODE.ORG http://www.ambion.com/techlib/ Company web site with very good technical resources including an excellent links page, summaries of recent papers on RNA- related topics, and free access to review articles and web features on RNA-related research topics. Ambion Inc. Technical Resources http://www.tigr.org/softlab/glimmer/glimmer.html Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non- commercial use. Glimmer http://asterias.bioinfo.cnio.es/ Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed. Asterias http://www.dkfz.de/spec/projekte/fragments/ GlycoFragment is a tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra. GlycoFragment Genomics http://bioserv.rpbs.jussieu.fr/cgi-bin/SABBAC Structural Alphabet based protein Backbone Builder from Alpha Carbon trace (SABBAC) is a tool for the reconstruction of complete protein structures from their alpha-carbon descriptions. SABBAC http://www.acaclone.com/ pDRAW32 is a multi-function tool with features including: graphical displays useful for drawing plasmids, sequence analysis and editing, virtual agarose gel plots and homology plots. pDRAW32