Bioinformatics Links

on the World Wide Web

International Nucleotide Sequence Database

• NCBI - National Center for Biotechnology Information (GenBank database and other stuff)
• EBI - European Bioinformatics Institute (EMBL database and other stuff)
• DDBJ - DNA Data Bank of Japan
• Feature Table Definition - the format of entries in these databases

Protein Sequence Databases

• SWISS-PROT & TrEMBL - annotated protein sequence database and computer annotated supplement
• PIR - Protein Information Resource
• MIPS - Munich Information centre for Protein Sequences

Database Searching by Sequence Similarity

• BLAST @ NCBI
• FASTA @ EBI
• Bioccelerator @ EMBL - rigorous Smith-Waterman database searches

Sequence Alignment

• NCBI - National Center for Biotechnology Information (GenBank database and other stuff)

• EBI - European Bioinformatics Institute (EMBL database and other stuff)

• DDBJ - DNA Data Bank of Japan

• Feature Table Definition - the format of entries in these databases

Protein Sequence Databases

• USC Sequence Alignment Server - align 2 sequences with all possible varieties of dynamic programming
• T-COFFEE - multiple sequence alignment
• ClustalW @ EBI - multiple sequence alignment
• MSA 2.1 - optimal multiple sequence alignment using the Carrillo-Lipman method
• BOXSHADE - pretty printing and shading of multiple alignments
• SIM4 - a program to align cDNA and genomic DNA
• Wise2 - align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools
• PipMaker - computes alignments of similar regions in two (long) DNA sequences
• VISTA - align + detect conserved regions in long genomic sequences

Human Genome Databases

• Celera's draft human & Drosophila genomes
• Draft Human Genome @ NCBI
• Draft Human Genome @ UCSC
• Ensembl - automatically annotated human genome
• GDB - Genome Database
• STACK - Sequence Tag Alignment and Consensus Knowledgebase
• GeneCards - human genes, proteins and diseases

Databases for Other Organisms

• GOLD - Genomes OnLine Database, information on complete and ongoing genome projects
• TIGR Comprehensive Microbial Resource
• TIGR Microbial Database
• The Proteome Databases - yeast and worm, good annotation
• Saccharomyces Genome Database
• The C. elegans Genome Project
• FlyBase
• Mouse Genome Informatics
• The Arabidopsis Information Resource
• ZFIN - Zebrafish Information Network
• DictyBase - Dictyostelium discoideum
• ECDC - E. coli database collection
• HIV sequence database

Protein Domain Families: Databases and Search Tools

• InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL

• PROSITE - database of protein families and domains

• Pfam - alignments and hidden Markov models covering many common protein domains

• SMART - analysis of domains in proteins

• ProDom - protein domain database

• PRINTS Database - groups of conserved motifs used to characterise protein families

• Blocks - multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins

• Protein Domain Profile Analysis @ BMERC - search a library of profiles with a protein sequence

• TIGRFAMs - yet more protein families based on Hidden Markov Models

Motif and Pattern Finding in Sequences

• Gibbs Motif Sampler - identification of conserved motifs in DNA or protein sequences
• AlignACE Homepage - gene regulatory motif finding
• MEME  - motif discovery and search in protein and DNA sequences
• SAM - tools for creating and using Hidden Markov Models
• Pratt - discover patterns in unaligned protein sequences

Protein 3D Structure Resources

• PDB - protein 3D structure database
• RasMol / Protein Explorer - molecule 3D structure viewers
• SCOP - Structural Classification Of Proteins
• UCL BSM CATH classification
• The DALI Domain Database
• FSSP - fold classification based on structure-structure alignment of proteins
• SWISS-MODEL - homology modeling server
• Structure Prediction Meta-server
• DALI - 3D structure alignment server
• Kenobi - protein structure alignment
• DSSP - defines secondary structure and solvent exposure from 3D coordinates
• HSSP Database - Homology-derived Secondary Structure of Proteins
• PredictProtein & PHD - predict secondary structure, solvent accessibility, transmembrane helices, and other stuff
• Jpred2 - protein secondary structure prediction
• PSIpred (& MEMSAT & GenTHREADER) - protein secondary structure prediction (& transmembrane helix prediction & tertiary structure prediction by threading)
• FlyBase
• Mouse Genome Informatics
• The Arabidopsis Information Resource
• ZFIN - Zebrafish Information Network
• DictyBase - Dictyostelium discoideum
• ECDC - E. coli database collection
• HIV sequence database

Gene Prediction

• Genscan – eukaryotes
• GeneMark
• Genie – eukaryotes
• GLIMMER – prokaryotes
• tRNAscan - SE 1.1 - search for tRNA genes in genomic sequence
• GFF (General Feature Format) Specification - a standard format for genomic sequence annotation

Gene Regulation Resources

• TRANSFAC - database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors

• EPD - eukaryotic promoter database
• SCPD - Saccharomyces cerevisiae promoter database
• RegulonDB - a database on transcriptional regulation in E. coli
• DPInteract - protein binding sites on E. coli DNA
• PromoterInspector - prediction of promoter regions in mammalian genomic sequences

• MatInspector - search for transcription factor binding sites
• Regulatory Sequence Analysis Tools

Metabolic, Gene Regulatory & Signal Transduction Network Databases

• KEGG - Kyoto Encyclopedia of Genes and Genomes
• BioCarta
• stke - Signal Transduction Knowledge Environment
• BIND - Biomolecular Interaction Network Database
• EcoCyc
• WIT
• SPAD - Signaling Pathway Database
• CSNDB - Cell Signalling Networks Database
• PathDB
• Transpath
• DIP - Database of Interacting Proteins
• PFBP - Protein Function and Biochemical Networks

• Alliance for Cellular Signalling

5 Big Genome Sequencing Centers

• Whitehead Institute for Biomedical Research/MIT Center for Genome Research
• The Sanger Centre
• University of Washington Genome Center
• Joint Genome Institute, U.S. Department of Energy
• Baylor College of Medicine Human Genome Sequencing Center

Phylogeny and Taxonomy

• The Tree of Life
• Species 2000 - index of the world's known species
• TreeBASE - a database of phylogenetic knowledge
• PHYLIP - package of programs for inferring phylogenies
• TreeView - user friendly tree displaying for Macs & Windows

• Bioinformatics at ISCB
• Bioinformatics at U. of Texas
• Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs
• COMPUTATIONAL MOLECULAR BIOLOGY, University of Washington
• Biomedical Informatics training program, Stanford University
• The UCLA Bioinformatics Graduate Program
• Graduate Studies in Computational Molecular Biology, Rutgers University
• Training in Bioinformatics and Computational Molecular Biology, Washington University
• W.M. Keck Center for Advanced Training in Computational Biology
• Professional Master of Science in Computational Molecular Biology, University of Southern California
• Undergraduate Degree Programs relating to Computational Biology, Carnegie Mellon University
• University of Pennsylvania Center for Bioinformatics
• Initiative in COMPUTATIONAL MOLECULAR BIOLOGY, Caltech
• The Merck Computational Biology and Chemistry Program at Carnegie Mellon University
• Bioinformatics and Computational Biology at George Mason University
• Bioinformatics Concentration Curriculum Requirements, George Mason University
• Bioinformatics Graduate Program, Boston University
  
• Masters of Science in Bioinformatics program, Georgia Tech
• Program in Computational Biology at Johns Hopkins University