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See also: [http://BioDatabase.Org MetaBase], the database database (also [[MetaBase]]).<br /><br /><strong>Genome Databases</strong><br /><br />Human<br /> OMIM (Mendelian Inheritance in Man) - http://www3.ncbi.nlm.nih.gov/Omim/<br /> GDB(Human Genome Data Base) - http://gdbwww.gdb.org/<br /> TIGR database - http://www.tigr.org/tdb/tdb.html<br /> Genethon database - http://www.genethon.fr/genethon_en.html<br />Mouse<br /> Eric Mercer's Mouse and Rat Home page - http://www.cco.caltech.edu:80/~mercer/htmls/rodent_page.html<br /> EUCIB Mouse Backcross Database (MBx) - http://www.hgmp.mrc.ac.uk/MBx/MBxHomepage.html<br /> Encyclopedia of the Mouse Genome - http://WWW.informatics.jax.org/encyclo.html<br /> MGD (Mouse Genome Database) - http://www.informatics.jax.org/mgd.html<br /> TBASE (Mouse Knockout Database) - http://www.gdb.org/Dan/tbase/tbase.html<br /> Gene Knockouts Pages - http://www.bayanet.com/bioscience/knockout/knochome.htm<br /> Mouse Cytogenetic Map Image - http://ws4.niai.affrc.go.jp/dbsearch2/mmap/mmap.html<br /> Whitehead Institute/MIT Genome Center Mouse Genetic Map - http://www-genome.wi.mit.edu/genome_data/mouse/mouse_index.html<br /> Portable Dictionary of the Mouse Genome - http://mickey.utmem.edu/front.html<br />Rat<br /> Rat Strain Information and Lab Code Names - http://www.anex.med.tokushima-u.ac.jp/index.html<br /> RATMAP - http://ratmap.gen.gu.se/<br /> Whitehead Institute/MIT Genome Center Rat SSLP Data - http://www-genome.wi.mit.edu:80/ftp/distribution/rat_sslp_releases/<br />Cow<br /> Bos taurus - http://keck.tamu.edu/cgi/bov/bov.html<br /> Cattle Genome Map - http://sol.marc.usda.gov/genome/cattle/cattle.html<br /> BovGBASE - http://tetra.gig.usda.gov:8400/bovgbase/manager.html<br /> Japan Cattle Cytogenetic Map - http://ws4.niai.affrc.go.jp/dbsearch2/cmap/cmap.html<br />Sheep<br /> USDA Sheep Genome Map - http://sol.marc.usda.gov/genome/sheep/sheep.html<br /> SheepBASE - http://tetra.gig.usda.gov:8400/sheepgbase/manager.html<br />Pig<br /> USDA Swine Genome Map - http://sol.marc.usda.gov/genome/swine/swine.html<br /> PiGBASE - http://tetra.gig.usda.gov:8400/pigbase/manager.html<br /> NAGRP Pig Gene Map - http://www.public.iastate.edu/~pigmap/pigmap.html<br /> Roslin PiGMaP Data - http://www.ri.bbsrc.ac.uk/pigmap/pigmap.html<br /> Pig Cytogenetic Map (Japan) - http://ws4.niai.affrc.go.jp/dbsearch2/pmap/pmap.html<br />Chicken<br /> Chicken Genome Map - http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html<br /> NAGRP Chicken Gene Map - http://poultry.mph.msu.edu/<br /> ChickGBASE - http://tetra.gig.usda.gov:8400/chickgbase/manager.html<br />Dog<br /> The Dog Genome Project - http://mendel.berkeley.edu/dog.html<br />Frog<br /><br /> Whole frog project - http://george.lbl.gov/ITG.hm.pg.docs/Whole.Frog/Whole.Frog.html<br />Zebra fish<br /> The Zebra Fish Server - http://zfish.uoregon.edu/<br /> Zebra Fish Information - http://golgi.harvard.edu/zebra.html<br />Other Vertebrates<br /> Agricultural Genomes - http://probe.nalusda.gov:8300/animal/index.html<br />Mosquito<br /> Mosquito genomic database - http://klab.agsci.colostate.edu/<br /> Mosquito Genomics WWW Server - http://klab.agsci.colostate.edu/<br />Drosophila<br /> Drosophila database - http://flybase.bio.indiana.edu/<br /> FlyDB - http://probe.nalusda.gov:8300/cgi-bin/dbrun/flydb?c<br /> Carthew Drosophila Lab - http://flies3.bio.pitt.edu/<br /> Nagoshi Lab Home Page (Drosophila) - http://fly2.biology.uiowa.edu/<br /> FlyView - A Drosophila Image Database - http://pbio07.uni-muenster.de/<br />Other Insects<br /> National Insect Genetic Resources - gopher://sol.ars-grin.gov/11/nigr<br /> Sericultural Science, the University of Tokyo - http://papilio.ab.a.u-tokyo.ac.jp/<br />Caenorhabditis elegans <br /> Caenorhabditis elegans WWW Server at UTSW - http://eatworms.swmed.edu/<br /> The C. elegans Genome Project FTP Site - http://www.sanger.ac.uk/~sjj/C.elegans_Home.html<br /> ACeDB, A Caenorhabditis elegans Database - http://moulon.inra.fr/acedb/acedb.html<br /> ACeDB browse - http://probe.nalusda.gov:8300/cgi-bin/browse/acedb<br /> wEST C. elegans Expressed Sequence Tag Database - gopher://gopher.gdb.org/77/.INDEX/west<br /> C. elegans repetitive DNA - http://ibc.wustl.edu/rpt/elegans<br /> CGC Caenorhabditis Genetics Center - gopher://elegans.cbs.umn.edu/77bin/cgcstrains.csh<br /> The Worm Web - http://sunflower.bio.indiana.edu:8080/wormweb.html<br /> David Baillie's Worm Lab - http://darwin.mbb.sfu.ca/imbb/dbaillie/baillielab.html<br /> Rose Worm Lab - http://genekit.medgen.ubc.ca/roselab.html<br />Fungal <br /> Mycology at Cornell - http://muse.bio.cornell.edu/taxonomy/fungi.html<br /> Saccharomyces genomic database - http://genome-www.stanford.edu/<br /> LISTA A Compilation of Sequences from Saccharomyces - gopher://gopher.gdb.org/77/.INDEX/lista<br /> Yeast Protein Database (YPD) - http://www.proteome.com/YPDhome.html<br /> MycDB Mycobacterium Database - http://www.biochem.kth.se/MycDB.html<br /> MycDB browse at NAL query - http://probe.nalusda.gov:8300/cgi-bin/browse/mycdb<br /> Candida albicans - http://alces.med.umn.edu/Candida.html<br /> FGSC Fungal Genetics Stock Center - http://s-ind2.dl.ac.uk/FGSC.html<br />Eschericia coli<br /> EcoCyc: Encyclopedia of E. coli Genes and Metabolism - http://www.ai.sri.com/ecocyc/browser.html<br /> ECDC (E. coli Database Collection) - http://susi.bio.uni-giessen.de/usr/local/www/html/ecdc.html<br />Bacillus subtilis<br /> NRSub (A Non-Redundant DNA Sequence Database for Bacillus subtilis) - http://ddbjs4h.genes.nig.ac.jp/<br />Other Prokaryotes<br /> Normalized Gene Designation Database (NGDD) - http://www.hgmp.mrc.ac.uk/local-data/Ngdd_form.html<br />Organellar<br /> Organelle Genome(A Sequence Database) - gopher://megasun.bch.umontreal.ca:70/11/Organelles/Genomes<br /> YAC Data searches - http://gc.bcm.tmc.edu:8088/bio/yac_search.html<br /> Mitochondrion - http://www.gen.emory.edu/mitomap.htm<br />Plant<br /> USDA/ARS/National Agricultural Library Plant Genome Data - gopher://gopher.nalusda.gov:70/11/infocntr/pltgen<br /> (NAL) National Agricultural Library; Plant Genomes - http://probe.nalusda.gov:8300/plant/index.html<br /> AAtDB browse An Arabidopsis thaliana genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/aatdb<br /> AAtDB at Harvard U. - http://weeds.mgh.harvard.edu/index.html<br /> Arabidopsis Expressed Sequence Tags (EST's) - gopher://weeds.mgh.harvard.edu/77/.index/ArabidopsisdbEST<br /> Arabidopsis Information Management System (AIMS) - http://genesys.cps.msu.edu:3333/<br /> U. Minnesota Arabidopsis cDNA sequencing Project - http://lenti.med.umn.edu/MSU.arab/arab_top_page.html<br /> Alfagenes browse Alfalfa genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/alfagenes<br /> BeanRef - http://www.uni-kl.de/FB-Biologie/Beanref/<br /> BeanGenes browse - http://probe.nalusda.gov:8300/cgi-bin/browse/beangenes<br /> ChlamyDB browse - http://probe.nalusda.gov:8300/cgi-bin/browse/chlamydb<br /> CottonDB browse Gossypium sp. database - http://probe.nalusda.gov:8300/cgi-bin/browse/cottondb<br /> GrainGenes browse - http://probe.nalusda.gov:8300/cgi-bin/browse/graingenes<br /> MaizeDB browse Maize genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/maizedb<br /> MaizeDB Maize Genome Database - http://www.agron.missouri.edu/<br /> RiceGenes browse Rice genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/ricegenes<br /> Japan Rice Genome Research Program (RGP) - http://www.staff.or.jp/<br /> SorghumDB browse Sorghum bicolor database - http://probe.nalusda.gov:8300/cgi-bin/browse/sorghumdb<br /> SoyBase browse Soybean genome database - http://probe.nalusda.gov:8300/cgi-bin/browse/soybase<br /> TreeGenes browse Forest trees database - http://probe.nalusda.gov:8300/cgi-bin/browse/treegenes<br /> Mendel browse Plant-wide gene names database - http://probe.nalusda.gov:8300/cgi-bin/browse/mendel<br />Comparative<br /> HOVERGEN (Database of Homologous Vertebrate Genes) - http://cammsg3.caos.kun.nl:8000/srs/srsc?-info+HOVERGEN<br /> The dysmorphic human and mouse homology database - http://www.hgmp.mrc.ac.uk/DHMHD/dysmorph.html<br /> XLocus - http://cgsc.biology.yale.edu/xlocus.html<br /> AGsDB A Genus Species Database - http://keck.tamu.edu/cgi/agsdb/agsdbserver.html<br /> The Homeobox Page - http://copan.bioz.unibas.ch/homeo.html<br /> Gene Family Database - http://gdbdoc.gdb.org/~avoltz/home.html<br /> XREFdb - http://www.ncbi.nlm.nih.gov/XREFdb/<br /> Online Mendelian Inheritance In Animals (OMIA) - http://morgan.angis.su.oz.au/BIRX/phenes_form.html<br /> Mammary knockout Database - http://mbcr.bcm.tmc.edu:80/BEP/ERMB/<br /><br /><br /><br /><strong>Protein Databases</strong><br /><br />Protein domain families: databases and search tools<br /> InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL - http://www.ebi.ac.uk/interpro/<br /> PSORT - prediction of protein sorting signals - http://psort.nibb.ac.jp/index.html<br /> Pfam - alignments and hidden Markov models covering many common protein domains - http://www.sanger.ac.uk/Software/Pfam/index.shtml<br /> SMART - analysis of domains in proteins - http://smart.embl-heidelberg.de/<br /> ProDom - protein domain database - http://prodes.toulouse.inra.fr/prodom/current/html/home.php<br /> PROSITE - database of protein families and domains - http://us.expasy.org/prosite/<br /> PRINTS - groups of conserved motifs used to characterise protein families - http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/<br /> ProfileScan - scans sequence against profile databases - http://myhits.isb-sib.ch/cgi-bin/motif_scan<br />Protein structure resources<br /> PDB - protein 3D structure database - http://www.rcsb.org/pdb/<br /> RasMol / Protein Explorer - molecule 3D structure viewers - http://www.umass.edu/microbio/rasmol/<br /> SCOP - Structural Classification Of Proteins - http://scop.mrc-lmb.cam.ac.uk/scop/<br /> FSSP - fold classification based on structure-structure alignment of proteins - http://www2.ebi.ac.uk/dali/fssp/fssp.html<br /> SWISS-MODEL - homology modeling server - http://www.expasy.ch/swissmod/SWISS-MODEL.html<br /> DALI - 3D structure alignment server - http://www2.ebi.ac.uk/dali/fssp/fssp.html<br /> DSSP - defines secondary structure and solvent exposure from 3D coordinates - http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html<br /> PredictProtein & PHD - sequence analysis and structure prediction - http://cubic.bioc.columbia.edu/predictprotein/<br /> TMpred - transmembrane helix prediction - http://www.ch.embnet.org/software/TMPRED_form.html<br /> TopPred 2 - Topology prediction of membrane proteins (Stockholm University) - http://www.sbc.su.se/~erikw/toppred2/<br /><br /><br /><strong><br />Genome Browsers and "complete" genomes</strong><br /> GenomeBrowser - human genome assembly and track browser at UCSC - http://genome.cse.ucsc.edu/<br /> Ensembl - genome assembly and browser at EBI/Sanger - http://www.ensembl.org/<br /> Map Viewer - human genome assembly and map viewer at NCBI - http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi<br /> Jax - mouse genomics at Jackson Laboratory - http://www.informatics.jax.org/<br /> RatMap - rat genome database at Goteborg - http://ratmap.gen.gu.se/<br /> Zfin - zebrafish information network and database project - http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg<br /> Flybase - database of drosophila genomics at Indiana - http://flybase.bio.indiana.edu/<br /> BDGP - fruit fly genomics center at Berkeley - http://www.fruitfly.org/<br /> WormBase - nematode mapping, sequencing and phenotypic repository - http://www.wormbase.org/<br /> SGD - yeast genome database - http://www.yeastgenome.org/<br /> TAIR - the arabidopsis information resource and tool center - http://arabidopsis.org/<br /> TIGR db - bacterial genomes at TIGR - http://www.tigr.org/tdb/mdb/mdbcomplete.html<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />