Bioinformatics DB

See also: MetaBase, the database database (also MetaBase).

Genome Databases

Human
    OMIM (Mendelian Inheritance in Man) - http://www3.ncbi.nlm.nih.gov/Omim/
    GDB(Human Genome Data Base) - http://gdbwww.gdb.org/
    TIGR database - http://www.tigr.org/tdb/tdb.html
    Genethon database - http://www.genethon.fr/genethon_en.html
Mouse
    Eric Mercer's Mouse and Rat Home page - http://www.cco.caltech.edu:80/~mercer/htmls/rodent_page.html
    EUCIB Mouse Backcross Database (MBx) - http://www.hgmp.mrc.ac.uk/MBx/MBxHomepage.html
    Encyclopedia of the Mouse Genome - http://WWW.informatics.jax.org/encyclo.html
    MGD (Mouse Genome Database) - http://www.informatics.jax.org/mgd.html
    TBASE (Mouse Knockout Database) - http://www.gdb.org/Dan/tbase/tbase.html
    Gene Knockouts Pages - http://www.bayanet.com/bioscience/knockout/knochome.htm
    Mouse Cytogenetic Map Image - http://ws4.niai.affrc.go.jp/dbsearch2/mmap/mmap.html
    Whitehead Institute/MIT Genome Center Mouse Genetic Map - http://www-genome.wi.mit.edu/genome_data/mouse/mouse_index.html
    Portable Dictionary of the Mouse Genome - http://mickey.utmem.edu/front.html
Rat
    Rat Strain Information and Lab Code Names - http://www.anex.med.tokushima-u.ac.jp/index.html
    RATMAP - http://ratmap.gen.gu.se/
    Whitehead Institute/MIT Genome Center Rat SSLP Data - http://www-genome.wi.mit.edu:80/ftp/distribution/rat_sslp_releases/
Cow
    Bos taurus - http://keck.tamu.edu/cgi/bov/bov.html
    Cattle Genome Map - http://sol.marc.usda.gov/genome/cattle/cattle.html
    BovGBASE - http://tetra.gig.usda.gov:8400/bovgbase/manager.html
    Japan Cattle Cytogenetic Map - http://ws4.niai.affrc.go.jp/dbsearch2/cmap/cmap.html
Sheep
    USDA Sheep Genome Map - http://sol.marc.usda.gov/genome/sheep/sheep.html
    SheepBASE - http://tetra.gig.usda.gov:8400/sheepgbase/manager.html
Pig
    USDA Swine Genome Map - http://sol.marc.usda.gov/genome/swine/swine.html
    PiGBASE - http://tetra.gig.usda.gov:8400/pigbase/manager.html
    NAGRP Pig Gene Map - http://www.public.iastate.edu/~pigmap/pigmap.html
    Roslin PiGMaP Data - http://www.ri.bbsrc.ac.uk/pigmap/pigmap.html
    Pig Cytogenetic Map (Japan) - http://ws4.niai.affrc.go.jp/dbsearch2/pmap/pmap.html
Chicken
    Chicken Genome Map - http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html
    NAGRP Chicken Gene Map - http://poultry.mph.msu.edu/
    ChickGBASE - http://tetra.gig.usda.gov:8400/chickgbase/manager.html
Dog
    The Dog Genome Project - http://mendel.berkeley.edu/dog.html
Frog

    Whole frog project - http://george.lbl.gov/ITG.hm.pg.docs/Whole.Frog/Whole.Frog.html
Zebra fish
    The Zebra Fish Server - http://zfish.uoregon.edu/
    Zebra Fish Information - http://golgi.harvard.edu/zebra.html
Other Vertebrates
    Agricultural Genomes - http://probe.nalusda.gov:8300/animal/index.html
Mosquito
    Mosquito genomic database - http://klab.agsci.colostate.edu/
    Mosquito Genomics WWW Server - http://klab.agsci.colostate.edu/
Drosophila
    Drosophila database - http://flybase.bio.indiana.edu/
    FlyDB - http://probe.nalusda.gov:8300/cgi-bin/dbrun/flydb?c
    Carthew Drosophila Lab - http://flies3.bio.pitt.edu/
    Nagoshi Lab Home Page (Drosophila) - http://fly2.biology.uiowa.edu/
    FlyView - A Drosophila Image Database - http://pbio07.uni-muenster.de/
Other Insects
    National Insect Genetic Resources - gopher://sol.ars-grin.gov/11/nigr
    Sericultural Science, the University of Tokyo - http://papilio.ab.a.u-tokyo.ac.jp/
Caenorhabditis elegans                                                                           
    Caenorhabditis elegans WWW Server at UTSW - http://eatworms.swmed.edu/
    The C. elegans Genome Project FTP Site - http://www.sanger.ac.uk/~sjj/C.elegans_Home.html
    ACeDB, A Caenorhabditis elegans Database - http://moulon.inra.fr/acedb/acedb.html
    ACeDB browse - http://probe.nalusda.gov:8300/cgi-bin/browse/acedb
    wEST  C. elegans Expressed Sequence Tag Database - gopher://gopher.gdb.org/77/.INDEX/west
    C. elegans repetitive DNA - http://ibc.wustl.edu/rpt/elegans
    CGC  Caenorhabditis Genetics Center - gopher://elegans.cbs.umn.edu/77bin/cgcstrains.csh
    The Worm Web - http://sunflower.bio.indiana.edu:8080/wormweb.html
    David Baillie's Worm Lab - http://darwin.mbb.sfu.ca/imbb/dbaillie/baillielab.html
    Rose Worm Lab - http://genekit.medgen.ubc.ca/roselab.html
Fungal                                                                                   
    Mycology at Cornell - http://muse.bio.cornell.edu/taxonomy/fungi.html
    Saccharomyces genomic database - http://genome-www.stanford.edu/
    LISTA  A Compilation of Sequences from Saccharomyces - gopher://gopher.gdb.org/77/.INDEX/lista
    Yeast Protein Database (YPD) - http://www.proteome.com/YPDhome.html
    MycDB  Mycobacterium Database - http://www.biochem.kth.se/MycDB.html
    MycDB browse at NAL query - http://probe.nalusda.gov:8300/cgi-bin/browse/mycdb
    Candida albicans - http://alces.med.umn.edu/Candida.html
    FGSC  Fungal Genetics Stock Center - http://s-ind2.dl.ac.uk/FGSC.html
Eschericia coli
    EcoCyc: Encyclopedia of E. coli Genes and Metabolism - http://www.ai.sri.com/ecocyc/browser.html
    ECDC (E. coli Database Collection) - http://susi.bio.uni-giessen.de/usr/local/www/html/ecdc.html
Bacillus subtilis
    NRSub (A Non-Redundant DNA Sequence Database for Bacillus subtilis) - http://ddbjs4h.genes.nig.ac.jp/
Other Prokaryotes
    Normalized Gene Designation Database (NGDD) - http://www.hgmp.mrc.ac.uk/local-data/Ngdd_form.html
Organellar
    Organelle Genome(A Sequence Database) - gopher://megasun.bch.umontreal.ca:70/11/Organelles/Genomes
    YAC Data searches - http://gc.bcm.tmc.edu:8088/bio/yac_search.html
    Mitochondrion - http://www.gen.emory.edu/mitomap.htm
Plant
    USDA/ARS/National Agricultural Library Plant Genome Data - gopher://gopher.nalusda.gov:70/11/infocntr/pltgen
    (NAL) National Agricultural Library; Plant Genomes - http://probe.nalusda.gov:8300/plant/index.html
    AAtDB browse An Arabidopsis thaliana genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/aatdb
    AAtDB at Harvard U. - http://weeds.mgh.harvard.edu/index.html
    Arabidopsis Expressed Sequence Tags (EST's) - gopher://weeds.mgh.harvard.edu/77/.index/ArabidopsisdbEST
    Arabidopsis Information Management System (AIMS) - http://genesys.cps.msu.edu:3333/
    U. Minnesota Arabidopsis cDNA sequencing Project - http://lenti.med.umn.edu/MSU.arab/arab_top_page.html
    Alfagenes browse Alfalfa genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/alfagenes
    BeanRef - http://www.uni-kl.de/FB-Biologie/Beanref/
    BeanGenes browse - http://probe.nalusda.gov:8300/cgi-bin/browse/beangenes
    ChlamyDB browse - http://probe.nalusda.gov:8300/cgi-bin/browse/chlamydb
    CottonDB browse Gossypium sp. database - http://probe.nalusda.gov:8300/cgi-bin/browse/cottondb
    GrainGenes browse - http://probe.nalusda.gov:8300/cgi-bin/browse/graingenes
    MaizeDB browse Maize genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/maizedb
    MaizeDB  Maize Genome Database - http://www.agron.missouri.edu/
    RiceGenes browse Rice genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/ricegenes
    Japan Rice Genome Research Program (RGP) - http://www.staff.or.jp/
    SorghumDB browse Sorghum bicolor database - http://probe.nalusda.gov:8300/cgi-bin/browse/sorghumdb
    SoyBase browse Soybean genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/soybase
    TreeGenes browse Forest trees database - http://probe.nalusda.gov:8300/cgi-bin/browse/treegenes
    Mendel browse Plant-wide gene names database - http://probe.nalusda.gov:8300/cgi-bin/browse/mendel
Comparative
    HOVERGEN (Database of Homologous Vertebrate Genes) - http://cammsg3.caos.kun.nl:8000/srs/srsc?-info+HOVERGEN
    The dysmorphic human and mouse homology database - http://www.hgmp.mrc.ac.uk/DHMHD/dysmorph.html
    XLocus - http://cgsc.biology.yale.edu/xlocus.html
    AGsDB  A Genus Species Database - http://keck.tamu.edu/cgi/agsdb/agsdbserver.html
    The Homeobox Page - http://copan.bioz.unibas.ch/homeo.html
    Gene Family Database - http://gdbdoc.gdb.org/~avoltz/home.html
    XREFdb - http://www.ncbi.nlm.nih.gov/XREFdb/
    Online Mendelian Inheritance In Animals (OMIA) - http://morgan.angis.su.oz.au/BIRX/phenes_form.html
    Mammary knockout Database - http://mbcr.bcm.tmc.edu:80/BEP/ERMB/



Protein Databases

Protein domain families: databases and search tools
    InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL - http://www.ebi.ac.uk/interpro/
    PSORT - prediction of protein sorting signals - http://psort.nibb.ac.jp/index.html
    Pfam - alignments and hidden Markov models covering many common protein domains - http://www.sanger.ac.uk/Software/Pfam/index.shtml
    SMART - analysis of domains in proteins - http://smart.embl-heidelberg.de/
    ProDom - protein domain database - http://prodes.toulouse.inra.fr/prodom/current/html/home.php
    PROSITE - database of protein families and domains - http://us.expasy.org/prosite/
    PRINTS - groups of conserved motifs used to characterise protein families - http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
    ProfileScan - scans sequence against profile databases - http://myhits.isb-sib.ch/cgi-bin/motif_scan
Protein structure resources
    PDB - protein 3D structure database - http://www.rcsb.org/pdb/
    RasMol / Protein Explorer - molecule 3D structure viewers - http://www.umass.edu/microbio/rasmol/
    SCOP - Structural Classification Of Proteins - http://scop.mrc-lmb.cam.ac.uk/scop/
    FSSP - fold classification based on structure-structure alignment of proteins - http://www2.ebi.ac.uk/dali/fssp/fssp.html
    SWISS-MODEL - homology modeling server - http://www.expasy.ch/swissmod/SWISS-MODEL.html
    DALI - 3D structure alignment server - http://www2.ebi.ac.uk/dali/fssp/fssp.html
    DSSP - defines secondary structure and solvent exposure from 3D coordinates - http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html
    PredictProtein & PHD -  sequence analysis and structure prediction - http://cubic.bioc.columbia.edu/predictprotein/
    TMpred - transmembrane helix prediction - http://www.ch.embnet.org/software/TMPRED_form.html
    TopPred 2 - Topology prediction of membrane proteins (Stockholm University) - http://www.sbc.su.se/~erikw/toppred2/



Genome Browsers and "complete" genomes
    GenomeBrowser - human genome assembly and track browser at UCSC - http://genome.cse.ucsc.edu/
    Ensembl - genome assembly and browser at EBI/Sanger - http://www.ensembl.org/
    Map Viewer - human genome assembly and map viewer at NCBI - http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi
    Jax - mouse genomics at Jackson Laboratory - http://www.informatics.jax.org/
    RatMap - rat genome database at Goteborg - http://ratmap.gen.gu.se/
    Zfin - zebrafish information network and database project - http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg
    Flybase - database of drosophila genomics at Indiana - http://flybase.bio.indiana.edu/
    BDGP - fruit fly genomics center at Berkeley - http://www.fruitfly.org/
    WormBase - nematode mapping, sequencing and phenotypic repository - http://www.wormbase.org/
    SGD - yeast genome database - http://www.yeastgenome.org/
    TAIR - the arabidopsis information resource and tool center - http://arabidopsis.org/
    TIGR db - bacterial genomes at TIGR - http://www.tigr.org/tdb/mdb/mdbcomplete.html