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 <