Table 1. Molecular Biology Database Collectiona

No.b
 Database name
 Full name and/or description
 URL
1. Nucleotide Sequence Databases
1.1. International Nucleotide Sequence Database Collaboration
1 DDBJ—DNA Data Bank of Japan All known nucleotide and protein sequences http://www.ddbj.nig.ac.jp/
2 EMBL Nucleotide Sequence Database All known nucleotide and protein sequences http://www.ebi.ac.uk/embl.html
3 GenBank® All known nucleotide and protein sequences http://www.ncbi.nlm.nih.gov/Entrez
1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
403 ACLAME A classification of genetic mobile elements http://aclame.ulb.ac.be/
30 CUTG Codon usage tabulated from GenBank http://www.kazusa.or.jp/codon/
480 Genetic Codes Genetic codes in various organisms and organelles http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
668 Entrez Gene Gene-centered information at NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
495 HERVd Human endogenous retrovirus database http://herv.img.cas.cz/
687 Hoppsigen Human and mouse homologous processed pseudogenes http://pbil.univ-lyon1.fr/databases/hoppsigen.html
294 Imprinted Gene Catalogue Imprinted genes and parent-of-origin effects in animals http://www.otago.ac.nz/IGC
512 Islander Pathogenicity islands and prophages in bacterial genomes http://www.indiana.edu/~islander
343 MICdb Prokaryotic microsatellites http://www.cdfd.org.in/micas
707 NPRD Nucleosome positioning region database http://srs6.bionet.nsc.ru/srs6/
47 STRBase Short tandem DNA repeats database http://www.cstl.nist.gov/div831/strbase/
5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml
48 Transterm Codon usage, start and stop signals http://uther.otago.ac.nz/Transterm.html
6 UniGene Non-redundant set of eukaryotic gene-oriented clusters http://www.ncbi.nlm.nih.gov/UniGene/
320 UniVec Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
302 VectorDB Characterization and classification of nucleic acid vectors http://genome-www2.stanford.edu/vectordb/
305 Xpro Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes http://origin.bic.nus.edu.sg/xpro/
1.2.2. Gene structure, introns and exons, splice sites
414 ASAP Alternative spliced isoforms http://www.bioinformatics.ucla.edu/ASAP
28 ASD Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb http://www.ebi.ac.uk/asd
10 ASDB Alternative splicing database: protein products and expression patterns of alternatively spliced genes http://hazelton.lbl.gov/~teplitski/alt
639 ASHESdb Alternatively spliced human genes by exon skipping database http://sege.ntu.edu.sg/wester/ashes/
450 EASED Extended alternatively spliced EST database http://eased.bioinf.mdc-berlin.de/
667 ECgene Genome annotation for alternative splicing http://genome.ewha.ac.kr/ECgene/
631 EDAS EST-derived alternative splicing database http://www.ig-msk.ru:8005/EDAS/
34 ExInt Exon–intron structure of eukaryotic genes http://sege.ntu.edu.sg/wester/exint/
36 HS3D Homo sapiens splice sites dataset http://www.sci.unisannio.it/docenti/rampone/
238 Intronerator Alternative splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
46 SpliceDB Canonical and non-canonical mammalian splice sites http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb
746 SpliceInfo Modes of alternative splicing in human genome http://140.115.50.96/SpliceInfo/
580 SpliceNest A tool for visualizing splicing of genes from EST data http://splicenest.molgen.mpg.de/
1.2.3. Transcriptional regulator sites and transcription factors
231 ACTIVITY Functional DNA/RNA site activity http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
31 DBTBS Bacillus subtilis promoters and transcription factors http://dbtbs.hgc.jp/
663 DoOP Database of orthologous promoters: chordates and plants http://doop.abc.hu/
106 DPInteract Binding sites for E.coli DNA-binding proteins http://arep.med.harvard.edu/dpinteract
33 EPD Eukaryotic promoter database http://www.epd.isb-sib.ch/
494 HemoPDB Hematopoietic promoter database: transcriptional regulation in hematopoiesis http://bioinformatics.med.ohio-state.edu/HemoPDB
516 JASPAR PSSMs for transcription factor DNA-binding sites http://jaspar.cgb.ki.se/
700 MAPPER Putative transcription factor binding sites in various genomes http://bio.chip.org/mapper
40 PLACE Plant cis-acting regulatory DNA elements http://www.dna.affrc.go.jp/htdocs/PLACE
41 PlantCARE Plant promoters and cis-acting regulatory elements http://intra.psb.ugent.be:8080/PlantCARE/
563 PlantProm Plant promoter sequences for RNA polymerase II http://mendel.cs.rhul.ac.uk/
566 PRODORIC Prokaryotic database of gene regulation networks http://prodoric.tu-bs.de/
42 PromEC E.coli promoters with experimentally identified transcriptional start sites http://bioinfo.md.huji.ac.il/marg/promec
246 SELEX_DB DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
227 TESS Transcription element search system http://www.cbil.upenn.edu/tess
756 TRACTOR db Transcription factors in gamma-proteobacteria database http://www.tractor.lncc.br/
345 TRANSCompel Composite regulatory elements affecting gene transcription in eukaryotes http://www.gene-regulation.com/pub/databases.html#transcompel
340 TRANSFAC Transcription factors and binding sites http://transfac.gbf.de/TRANSFAC/index.html
757 TRED Transcriptional regulatory element database http://rulai.cshl.edu/tred
49 TRRD Transcription regulatory regions of eukaryotic genes http://www.bionet.nsc.ru/trrd/
2. RNA sequence databases
229 16S and 23S rRNA Mutation Database 16S and 23S ribosomal RNA mutations http://www.fandm.edu/Departments/Biology/Databases/RNA.html
230 5S rRNA Database 5S rRNA sequences http://biobases.ibch.poznan.pl/5SData/
411 Aptamer database Small RNA/DNA molecules binding nucleic acids, proteins http://aptamer.icmb.utexas.edu/
232 ARED AU-rich element-containing mRNA database http://rc.kfshrc.edu.sa/ared
378 Mobile group II introns A database of group II introns, self-splicing catalytic RNAs http://www.fp.ucalgary.ca/group2introns/
463 European rRNA database All complete or nearly complete rRNA sequences http://www.psb.ugent.be/rRNA/
490 GtRDB Genomic tRNA database http://rna.wustl.edu/GtRDB
236 Guide RNA Database RNA editing in various kinetoplastid species http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
76 HIV Sequence Database HIV RNA sequences http://hiv-web.lanl.gov/
689 HuSiDa Human siRNA database http://itb1.biologie.hu-berlin.de/~nebulus/sirna/
237 HyPaLib Hybrid pattern library: structural elements in classes of RNA http://bibiserv.techfak.uni-bielefeld.de/HyPa/
379 IRESdb Internal ribosome entry site database http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
529 microRNA Registry Database of microRNAs (small non-coding RNAs) http://www.sanger.ac.uk/Software/Rfam/mirna/
380 NCIR Non-canonical interactions in RNA structures http://prion.bchs.uh.edu/bp_type/
381 ncRNAs Database Non-coding RNAs with regulatory functions http://biobases.ibch.poznan.pl/ncRNA/
705 NONCODE A database of non-coding RNAs http://www.bioinfo.org.cn/NONCODE/index.htm
240 PLANTncRNAs Plant non-coding RNAs http://www.prl.msu.edu/PLANTncRNAs
564 Plant snoRNA DB snoRNA genes in plant species http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
723 PolyA_DB A database of mammalian mRNA polyadenylation http://polya.umdnj.edu/polyadb/
242 PseudoBase Database of RNA pseudoknots http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
382 Rfam Non-coding RNA families http://www.sanger.ac.uk/Software/Rfam/
244 RISSC Ribosomal internal spacer sequence collection http://ulises.umh.es/RISSC
630 RNAdb Mammalian non-coding RNA database http://ncrna.bioinformatics.com.au/
245 RNA Modification Database Naturally modified nucleosides in RNA http://medlib.med.utah.edu/RNAmods/
43 RRNDB rRNA operon numbers in various prokaryotes http://rrndb.cme.msu.edu/
629 siRNAdb siRNA database and search engine http://sirna.cgb.ki.se/
247 Small RNA Database Small RNAs from prokaryotes and eukaryotes http://mbcr.bcm.tmc.edu/smallRNA
248 SRPDB Signal recognition particle database http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
754 SSU rRNA Modification Database Modified nucleosides in small subunit rRNA http://medstat.med.utah.edu/SSUmods/
383 Subviral RNA Database Viroids and viroid-like RNAs http://subviral.med.uottawa.ca/
249 tmRNA Website tmRNA sequences and alignments http://www.indiana.edu/~tmrna
250 tmRDB tmRNA database http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
251 tRNA sequences tRNA viewer and sequence editor http://www.uni-bayreuth.de/departments/biochemie/trna/
252 UTRdb/UTRsite 5'- and 3'-UTRs of eukaryotic mRNAs http://bighost.area.ba.cnr.it/srs6/
3. Protein sequence databases
3.1. General sequence databases
163 EXProt Sequences of proteins with experimentally verified function http://www.cmbi.kun.nl/EXProt/
542 NCBI Protein database All protein sequences: translated from GenBank and imported from other protein databases http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
714 PA-GOSUB Protein sequences from model organisms, GO assignment and subcellular localization http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
194 PIR-PSD Protein information resource protein sequence database, has been merged into the UniProt knowledgebase http://pir.georgetown.edu/
370 PIR-NREF PIR's non-redundant reference protein database http://pir.georgetown.edu/pirwww/pirnref.shtml
565 PRF Protein research foundation database of peptides: sequences, literature and unnatural amino acids http://www.prf.or.jp/en
197 Swiss-Prot Now UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase http://www.expasy.org/sprot
198 TrEMBL Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase http://www.expasy.org/sprot
775 UniParc UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence http://www.uniprot.org/database/archive.shtml
318 UniProt Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases http://www.uniprot.org/
776 UniRef UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms) http://www.uniprot.org/database/nref.shtml
3.2. Protein properties
221 AAindex Physicochemical properties of amino acids
729 ProNIT Thermodynamic data on protein–nucleic acid interactions http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
280 ProTherm Thermodynamic data for wild-type and mutant proteins http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
772 TECRdb Thermodynamics of enzyme-catalyzed reactions http://xpdb.nist.gov/enzyme_thermodynamics/
3.3. Protein localization and targeting
444 DBSubLoc Database of protein subcellular localization http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
375 NESbase Nuclear export signals database http://www.cbs.dtu.dk/databases/NESbase
376 NLSdb Nuclear localization signals http://cubic.bioc.columbia.edu/db/NLSdb/
704 NMPdb Nuclear matrix associated proteins database http://www.rostlab.org/db/NMPdb/
706 NOPdb Nucleolar proteome database http://www.lamondlab.com/NOPdb/
734 PSORTdb Protein subcellular localization in bacteria http://db.psort.org/
745 SPD Secreted protein database http://spd.cbi.pku.edu.cn/
587 THGS Transmembrane helices in genome sequences http://pranag.physics.iisc.ernet.in/thgs/
589 TMPDB Experimentally characterized transmembrane topologies http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
3.4. Protein sequence motifs and active sites
374 ASC Active sequence collection: biologically active peptides http://bioinformatica.isa.cnr.it/ASC/
203 Blocks Alignments of conserved regions in protein families http://blocks.fhcrc.org/
440 CSA Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure http://www.ebi.ac.uk/thornton-srv/databases/CSA/
438 COMe Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins) http://www.ebi.ac.uk/come
771 CopS Comprehensive peptide signature database http://203.195.151.46/copsv2/index.html
666 eBLOCKS Highly conserved protein sequence blocks http://fold.stanford.edu/eblocks/acsearch.html
206 eMOTIF Protein sequence motif determination and searches http://motif.stanford.edu/emotif
179 Metalloprotein Site Database Metal-binding sites in metalloproteins http://metallo.scripps.edu/
209 O-GlycBase O- and C-linked glycosylation sites in proteins http://www.cbs.dtu.dk/databases/OGLYCBASE/
717 PDBSite 3D structure of protein functional sites http://srs6.bionet.nsc.ru/srs6/
187 Phospho.ELM S/T/Y protein phosphorylation sites (formerly PhosphoBase) http://phospho.elm.eu.org/
193 PROMISE Prosthetic centers and metal ions in protein active sites http://metallo.scripps.edu/PROMISE
215 PROSITE Biologically significant protein patterns and profiles http://www.expasy.org/prosite
732 ProTeus Signature sequences at the protein N- and C-termini http://www.proteus.cs.huji.ac.il/
3.5. Protein domain databases; protein classification
622 ADDA A database of protein domain classification http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
204 CDD Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
205 CluSTr Clusters of Swiss-Prot+TrEMBL proteins http://www.ebi.ac.uk/clustr
671 FunShift Functional divergence between the subfamilies of a protein domain family http://funshift.cgb.ki.se/
200 Hits A database of protein domains and motifs http://hits.isb-sib.ch/
207 InterPro Integrated resource of protein families, domains and functional sites http://www.ebi.ac.uk/interpro
208 iProClass Integrated protein classification database http://pir.georgetown.edu/iproclass/
561 PIRSF Family/superfamily classification of whole proteins http://pir.georgetown.edu/pirsf/
212 PRINTS Hierarchical gene family fingerprints http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
210 Pfam Protein families: multiple sequence alignments and profile hidden Markov models of protein domains http://www.sanger.ac.uk/Software/Pfam/
727 PRECISE Predicted and consensus interaction sites in enzymes http://precise.bu.edu/precisedb/
214 ProDom Protein domain families http://www.toulouse.inra.fr/prodom.html
216 ProtoMap Hierarchical classification of Swiss-Prot proteins http://protomap.cornell.edu/
567 ProtoNet Hierarchical clustering of Swiss-Prot proteins http://www.protonet.cs.huji.ac.il/
740 S4 Structure-based sequence alignments of SCOP superfamilies http://compbio.mds.qmw.ac.uk/~james/S4.shtml
217 SBASE Protein domain sequences and tools http://www.icgeb.org/sbase
218 SMART Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains http://smart.embl-heidelberg.de/
219 SUPFAM Grouping of sequence families into superfamilies http://pauling.mbu.iisc.ernet.in/~supfam
220 SYSTERS Systematic re-searching and clustering of proteins http://systers.molgen.mpg.de/
199 TIGRFAMs TIGR protein families adapted for functional annotation http://www.tigr.org/TIGRFAMs
3.6. Databases of individual protein families
156 AARSDB Aminoacyl-tRNA synthetase database http://rose.man.poznan.pl/aars/index.html
308 ASPD Artificial selected proteins/peptides database http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
158 BacTregulators Transcriptional regulators of AraC and TetR families http://www.bactregulators.org/
364 CSDBase Cold shock domain-containing proteins http://www.chemie.uni-marburg.de/~csdbase/
653 CuticleDB Structural proteins of Arthropod cuticle http://bioinformatics.biol.uoa.gr/cuticleDB
658 DCCP Database of copper-chelating proteins http://sdbi.sdut.edu.cn/DCCP/en/index.php
160 DExH/D Family Database DEAD-box, DEAH-box and DExH-box proteins http://www.helicase.net/dexhd/dbhome.htm
161 Endogenous GPCR List G protein-coupled receptors; expression in cell lines http://www.tumor-gene.org/GPCR/gpcr.html
162 ESTHER Esterases and other alpha/beta hydrolase enzymes http://www.ensam.inra.fr/esther
464 EyeSite Families of proteins functioning in the eye http://eyesite.cryst.bbk.ac.uk/
166 GPCRDB G protein-coupled receptors database http://www.gpcr.org/7tm/
679 gpDB G-proteins and their interaction with GPCRs http://bioinformatics.biol.uoa.gr/gpDB
167 Histone Database Histone fold sequences and structures http://research.nhgri.nih.gov/histones/
169 Homeobox Page Homeobox proteins, classification and evolution http://www.biosci.ki.se/groups/tbu/homeo.html
293 Hox-Pro Homeobox genes database http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
170 Homeodomain Resource Homeodomain sequences, structures and related genetic and genomic information http://research.nhgri.nih.gov/homeodomain/
366 HORDE Human olfactory receptor data exploratorium http://bioinfo.weizmann.ac.il/HORDE/
174 InBase Inteins (protein splicing elements) database: properties, sequences, bibliography http://www.neb.com/neb/inteins.html
518 KinG—Kinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes http://hodgkin.mbu.iisc.ernet.in/~king
519 Knottins Database of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot http://knottin.cbs.cnrs.fr/
176 LGICdb Ligand-gated ion channel subunit sequences database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
368 Lipase Engineering Database Sequence, structure and function of lipases and esterases http://www.led.uni-stuttgart.de/
524 LOX-DB Mammalian, invertebrate, plant and fungal lipoxygenases http://www.dkfz-heidelberg.de/spec/lox-db/
177 MEROPS Database of proteolytic enzymes (peptidases) http://merops.sanger.ac.uk/
369 NPD Nuclear protein database http://npd.hgu.mrc.ac.uk/
546 NucleaRDB Nuclear receptor superfamily http://www.receptors.org/NR/
182 Nuclear Receptor Resource Nuclear receptor superfamily http://nrr.georgetown.edu/NRR/nrrhome.htm
183 NUREBASE Nuclear hormone receptors database http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
184 Olfactory Receptor Database Sequences for olfactory receptor-like molecules http://senselab.med.yale.edu/senselab/ordb/
185 ooTFD Object-oriented transcription factors database http://www.ifti.org/ootfd
188 PKR Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties http://pkr.sdsc.edu/html/index.shtml
759 PLPMDB Pyridoxal-5'-phosphate dependent enzymes mutations http://www.studiofmp.com/plpmdb/
609 ProLysED A database of bacterial protease systems http://genome.ukm.my/prolyses/
192 Prolysis Proteases and natural and synthetic protease inhibitors http://delphi.phys.univ-tours.fr/Prolysis/
224 REBASE Restriction enzymes and associated methylases http://rebase.neb.com/rebase/rebase.html
195 Ribonuclease P Database RNase P sequences, alignments and structures http://www.mbio.ncsu.edu/RNaseP/home.html
573 RPG Ribosomal protein gene database http://ribosome.miyazaki-med.ac.jp/
575 RTKdb Receptor tyrosine kinase sequences http://pbil.univ-lyon1.fr/RTKdb/
309 S/MARt dB Nuclear scaffold/matrix attached regions http://smartdb.bioinf.med.uni-goettingen.de/
741 Scorpion Database of scorpion toxins http://research.i2r.a-star.edu.sg:8080/scorpion/
372 SDAP Structural database of allergenic proteins and food allergens http://fermi.utmb.edu/SDAP
196 SENTRA Sensory signal transduction proteins http://www-wit.mcs.anl.gov/sentra/
373 SEVENS 7-transmembrane helix receptors (G-protein-coupled) http://sevens.cbrc.jp/
248 SRPDB Proteins of the signal recognition particles http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
314 TrSDB Transcription factor database http://ibb.uab.es/trsdb
399 VKCDB Voltage-gated potassium channel database http://vkcdb.biology.ualberta.ca/
202 Wnt Database Wnt proteins and phenotypes http://www.stanford.edu/~rnusse/wntwindow.html
4. Structure Databases
4.1. Small molecules
646 ChEBI Chemical entities of biological interest http://www.ebi.ac.uk/chebi/
261 CSD Cambridge structural database: crystal structure information for organic and metal-organic compounds http://www.ccdc.cam.ac.uk/prods/csd/csd.html
265 HIC-Up Hetero-compound Information Centre—Uppsala http://xray.bmc.uu.se/hicup
402 AANT Amino acid–nucleotide interaction database http://aant.icmb.utexas.edu/
111 Klotho Collection and categorization of biological compounds http://www.biocheminfo.org/klotho
113 LIGAND Chemical compounds and reactions in biological pathways
615 PDB-Ligand 3D structures of small molecules bound to proteins and nucleic acids http://www.idrtech.com/PDB-Ligand/
735 PubChem Structures and biological activities of small organic molecules http://pubchem.ncbi.nlm.nih.gov/
4.2. Carbohydrates
429 CCSD Complex carbohydrate structure database (CarbBank) http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
652 CSS Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB http://www.dkfz.de/spec/css/
486 Glycan Carbohydrate database, part of the KEGG system
292 GlycoSuiteDB N- and O-linked glycan structures and biological sources http://www.glycosuite.com/
535 Monosaccharide Browser Space-filling Fischer projections of monosaccharides http://www.jonmaber.demon.co.uk/monosaccharide
300 SWEET-DB Annotated carbohydrate structure and substance information http://www.dkfz-heidelberg.de/spec2/sweetdb/
4.3. Nucleic acid structure
272 NDB Nucleic acid-containing structures http://ndbserver.rutgers.edu/
273 NTDB Thermodynamic data for nucleic acids http://ntdb.chem.cuhk.edu.hk/
387 RNABase RNA-containing structures from PDB and NDB http://www.rnabase.org/
283 SCOR Structural classification of RNA: RNA motifs by structure, function and tertiary interactions http://scor.lbl.gov/
4.4. Protein structure
413 ArchDB Automated classification of protein loop structures http://gurion.imim.es/archdb
255 ASTRAL Sequences of domains of known structure, selected subsets and sequence–structure correspondences http://astral.stanford.edu/
288 BAliBASE A database for comparison of multiple sequence alignments http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
257 BioMagResBank NMR spectroscopic data for proteins and nucleic acids http://www.bmrb.wisc.edu/
384 CADB Conformational angles in proteins database http://cluster.physics.iisc.ernet.in/cadb/
258 CATH Protein domain structures database http://www.biochem.ucl.ac.uk/bsm/cath_new
259 CE 3D protein structure alignments http://cl.sdsc.edu/ce.html
260 CKAAPs DB Structurally similar proteins with dissimilar sequences http://ckaap.sdsc.edu/
442 Dali Protein fold classification using the Dali search engine http://www.bioinfo.biocenter.helsinki.fi:8080/dali/
385 Decoys ‘R’ Us Computer-generated protein conformations http://dd.stanford.edu/
447 DisProt Database of Protein Disorder: proteins that lack fixed 3D structure in their native states http://divac.ist.temple.edu/disprot
448 DomIns Domain insertions in known protein structures http://stash.mrc-lmb.cam.ac.uk/DomIns
264 DSDBASE Native and modeled disulfide bonds in proteins http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
386 DSMM Database of simulated molecular motions http://projects.villa-bosch.de/dbase/dsmm/
452 eF-site Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites http://ef-site.protein.osaka-u.ac.jp/eF-site
674 GenDiS Genomic distribution of protein structural superfamilies http://caps.ncbs.res.in/gendis/home.html
472 Gene3D Precalculated structural assignments for whole genomes http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
489 GTD Genomic threading database: structural annotations of complete proteomes http://bioinf.cs.ucl.ac.uk/GTD
322 GTOP Protein fold predictions from genome sequences http://spock.genes.nig.ac.jp/~genome/
360 Het-PDB Navi Hetero-atoms in protein structures http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
498 HOMSTRAD Homologous structure alignment database: curated structure-based alignments for protein families http://www-cryst.bioc.cam.ac.uk/homstrad
267 IMB Jena Image Library Visualization and analysis of 3D biopolymer structures http://www.imb-jena.de/IMAGE.html
502 IMGT/3Dstructure-DB Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins http://imgt3d.igh.cnrs.fr/
268 ISSD Integrated sequence–structure database http://www.protein.bio.msu.su/issd
269 LPFC Library of protein family core structures http://www-smi.stanford.edu/projects/helix/LPFC
270 MMDB NCBI's database of 3D structures, part of NCBI Entrez http://www.ncbi.nlm.nih.gov/Structure
456 E-MSD EBI's macromolecular structure database http://www.ebi.ac.uk/msd
331 ModBase Annotated comparative protein structure models http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
262 MolMovDB Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies http://bioinfo.mbb.yale.edu/MolMovDB/
274 PALI Phylogeny and alignment of homologous protein structures http://pauling.mbu.iisc.ernet.in/~pali
275 PASS2 Structural motifs of protein superfamilies http://ncbs.res.in/~faculty/mini/campass/pass.html
557 PepConfDB A database of peptide conformations http://www.peptidome.org/products/list.htm
276 PDB Protein structure databank: all publicly available 3D structures of proteins and nucleic acids http://www.rcsb.org/pdb
277 PDB-REPRDB Representative protein chains, based on PDB entries http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
278 PDBsum Summaries and analyses of PDB structures http://www.biochem.ucl.ac.uk/bsm/pdbsum
619 PDB_TM Transmembrane proteins with known 3D structure http://www.enzim.hu/PDB_TM/
719 Protein Folding Database Experimental data on protein folding http://pfd.med.monash.edu.au/
282 SCOP Structural classification of proteins http://scop.mrc-lmb.cam.ac.uk/scop
284 Sloop Classification of protein loops http://www-cryst.bioc.cam.ac.uk/~sloop/
583 Structure Superposition Database Pairwise superposition of TIM-barrel structures http://ssd.rbvi.ucsf.edu/
585 SWISS-MODEL Repository Database of annotated 3D protein structure models http://swissmodel.expasy.org/repository
285 SUPERFAMILY Assignments of proteins to structural superfamilies http://supfam.org/
584 SURFACE Surface residues and functions annotated, compared and evaluated: a database of protein surface patches http://cbm.bio.uniroma2.it/surface
764 TargetDB Target data from worldwide structural genomics projects http://targetdb.pdb.org/
401 3D-GENOMICS Structural annotations for complete proteomes http://www.sbg.bio.ic.ac.uk/3dgenomics
310 TOPS Topology of protein structures database http://www.tops.leeds.ac.uk/
5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature
73 Genew Human gene nomenclature: approved gene symbols http://www.gene.ucl.ac.uk/nomenclature
487 GO Gene ontology consortium database http://www.geneontology.org/
389 GOA EBI's gene ontology annotation project http://www.ebi.ac.uk/GOA
513 IUBMB Nomenclature database Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins http://www.chem.qmul.ac.uk/iubmb
514 IUPAC Nomenclature database Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission http://www.chem.qmul.ac.uk/iupac
515 IUPHAR-RD The International Union of Pharmacology recommendations on receptor nomenclature and drug classification http://www.iuphar-db.org/iuphar-rd/
552 PANTHER Gene products organized by biological function http://panther.celera.com/
317 UMLS Unified medical language system http://umlsks.nlm.nih.gov/
5.1.1. Taxonomy and Identification
78 ICB gyrB database for identification and classification of bacteria http://seasquirt.mbio.co.jp/icb/index.php
297 NCBI Taxonomy Names of all organisms represented in GenBank http://www.ncbi.nlm.nih.gov/Taxonomy/
608 PANDIT Protein and associated nucleotide domains with inferred trees http://www.ebi.ac.uk/goldman-srv/pandit/
299 RIDOM rRNA-based differentiation of medical microorganisms http://www.ridom-rdna.de/
243 RDP-II Ribosomal database project http://rdp.cme.msu.edu/
301 Tree of Life Information on phylogeny and biodiversity http://phylogeny.arizona.edu/tree/phylogeny.html
5.2. General genomics databases
7 COG Clusters of orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG
650 COGENT Complete genome tracking: predicted peptides from fully sequenced genomes http://maine.ebi.ac.uk:8000/services/cogent/
337 CORG Comparative regulatory genomics: conserved non-coding sequence blocks http://corg.molgen.mpg.de/
445 DEG Database of essential genes from bacteria and yeast http://tubic.tju.edu.cn/deg
451 EBI Genomes EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://www.ebi.ac.uk/genomes
453 EGO Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices http://www.tigr.org/tdb/tgi/ego/
70 EMGlib Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms http://pbil.univ-lyon1.fr/emglib/emglib.html
458 Entrez Genomes NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
461 ERGOLight Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database http://www.ergo-light.com/ERGO
470 FusionDB Database of bacterial and archaeal gene fusion events http://igs-server.cnrs-mrs.fr/FusionDB
611 Genome Atlas DNA structural properties of sequenced genomes http://www.cbs.dtu.dk/services/GenomeAtlas/
484 Genome Information Broker DDBJ's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://gib.genes.nig.ac.jp/
678 Genome Reviews Integrated view of complete genomes http://www.ebi.ac.uk/GenomeReviews/
75 GOLD Genomes online database: a listing of completed and ongoing genome projects http://www.genomesonline.org/
352 HGT-DB Putative horizontally transferred genes in prokaryotic genomes http://www.fut.es/~debb/HGT/
223 Integr8 Functional classification of proteins in whole genomes http://www.ebi.ac.uk/integr8/
112 KEGG Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways http://www.genome.jp/kegg
528 MBGD Microbial genome database for comparative analysis
549 ORFanage Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes http://www.cs.bgu.ac.il/~nomsiew/ORFans
551 PACRAT Archaeal and bacterial intergenic sequence features http://www.biosci.ohio-tate.edu/~pacrat
715 PartiGeneDB Assembled partial genomes for ~250 eukaryotic organisms http://www.partigenedb.org/
354 PEDANT Results of an automated analysis of genomic sequences http://pedant.gsf.de/
99 TIGR Microbial Database Lists of completed and ongoing genome projects with links to complete genome sequences http://www.tigr.org/tdb/mdb/mdbcomplete.html
66 TIGR Comprehensive Microbial Resource Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins http://www.tigr.org/CMR
311 TransportDB Predicted membrane transporters in complete genomes, classified according to the TC classification system http://www.membranetransport.org/
118 WIT3 What is there? Metabolic reconstruction for completely sequenced microbial genomes http://www-wit.mcs.anl.gov/wit3/
5.3. Organism-specific databases
5.3.1. Viruses
473 HCVDB The hepatitis C virus database http://hepatitis.ibcp.fr/
497 HIV Drug Resistance Database HIV mutations that confer resistance to anti-HIV drugs http://resdb.lanl.gov/Resist_DB/default.htm
168 HIV Molecular Immunology Database HIV epitopes http://hiv-web.lanl.gov/immunology/
365 HIV RT and Protease Sequence Database HIV reverse transcriptase and protease sequences http://hivdb.stanford.edu/
602 NCBI Viral Genomes Viral genome resource at NCBI http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html
725 Poxvirus.org Poxvirus genomic sequences and gene annotation http://www.poxvirus.org/
750 T4-like genome database Sequences of T4-like bacteriophages from various sources http://phage.bioc.tulane.edu/
201 VIDA Homologous viral protein families database http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
761 VIPER Virus particle explorer: virus capsid structures http://mmtsb.scripps.edu/viper
303 VirOligo Virus-specific oligonucleotides for PCR and hybridization http://viroligo.okstate.edu/
5.3.2. Prokaryotes
641 BacMap Picture atlas of annotated bacterial genomes http://wishart.biology.ualberta.ca/BacMap
614 MetaGrowth Growth requirements of bacterial pathogens http://igs-server.cnrs-mrs.fr/axenic/
720 PGTdb Prokaryotic growth temperature database http://pgtdb.csie.ncu.edu.tw/
5.3.2.1. Escherichia coli
415 ASAP A systematic annotation package for community analysis of E.coli and related genomes https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
428 CyberCell database A collection of data on E.coli K12 intended for mathematical modeling to simulate the bacterial cell http://redpoll.pharmacy.ualberta.ca/CCDB
436 coliBase A database for E.coli, Salmonella and Shigella http://colibase.bham.ac.uk/
437 Colibri E.coli genome database at Institut Pasteur http://genolist.pasteur.fr/Colibri/
623 EchoBASE Post-genomic studies of Escherichia coli http://www.ecoli-york.org/
462 Essential genes in E.coli First results of an E.coli gene deletion project http://www.genome.wisc.edu/resources/essential.htm
482 GenoBase E.coli genome database at Nara Institute http://ecoli.aist-nara.ac.jp/
165 GenProtEC E.coli K12 genome and proteome database http://genprotec.mbl.edu/
555 PEC Profiling of E.coli chromosome http://shigen.lab.nig.ac.jp/ecoli/pec
108 EcoCyc E.coli K12 genes, metabolic pathways, transporters and gene regulation http://ecocyc.org/
69 EcoGene Sequence and literature data on E.coli genes and proteins http://bmb.med.miami.edu/EcoGene/EcoWeb/
116 RegulonDB Transcriptional regulation and operon organization in E.coli http://www.cifn.unam.mx/Computational_Genomics/regulondb/
5.3.2.2. Bacillus subtilis
424 BSORF Bacillus subtilis genome database at Kyoto U.
89 NRSub Non-redundant Bacillus subtilis database at U. Lyon http://pbil.univ-lyon1.fr/nrsub/nrsub.html
96 SubtiList Bacillus subtilis genome database at Institut Pasteur http://genolist.pasteur.fr/SubtiList/
5.3.2.3. Other bacteria
420 BioCyc Pathway/genome databases for many bacteria http://biocyc.org/
426 CampyDB Database for Campylobacter genome analysis http://campy.bham.ac.uk/
433 ClostriDB Finished and unfinished genomes of Clostridium spp. http://clostri.bham.ac.uk/
648 CIDB Chlamydia Interactive Database: gene expression data http://www.it.deakin.edu.au/CIDB
68 CyanoBase Cyanobacterial genomes http://www.kazusa.or.jp/cyano
521 LeptoList Leptospira interrogans genome http://bioinfo.hku.hk/LeptoList
534 MolliGen Genomic data on mollicutes http://cbi.labri.fr/outils/molligen/
733 PseudoCAP Pseudomonas aeruginosa genome database and community annotation project http://www.pseudomonas.com/
94 RsGDB Rhodobacter sphaeroides genome http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/
762 VirFact Bacterial virulence factors and pathogenicity islands http://virfact.burnham.org/
760 Virulence Factors Reference database for microbial virulence factors http://zdsys.chgb.org.cn/VFs/main.htm
5.3.3. Unicellular eukaryotes
409 ApiEST-DB EST sequences from various Apicomplexan parasites http://www.cbil.upenn.edu/paradbs-servlet
439 CryptoDB Cryptosporidium parvum genome database http://cryptodb.org/
662 Diatom EST Database ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum http://avesthagen.sznbowler.com/
446 DictyBase Universal resource for Dictyostelium discoideum http://dictybase.org/
72 Full-Malaria Full-length cDNA library from erythrocytic-stage Plasmodium falciparum http://fullmal.ims.u-tokyo.ac.jp/
328 GeneDB Curated database for various Sanger-sequenced genomes http://www.genedb.org/
698 LumbriBASE ESTs of the earthworm Lumbricus rubellus http://www.earthworms.org/
91 PlasmoDB Plasmodium genome database http://plasmodb.org/
586 TcruziDB Trypanosoma cruzi genome database http://tcruzidb.org/
359 ToxoDB Toxoplasma gondii genome database http://toxodb.org/
5.3.4. Fungi
5.3.4.1. Yeasts
635 AGD Ashbya gossypii genome database http://agd.unibas.ch/
617 CandidaDB Candida albicans genome database http://genolist.pasteur.fr/CandidaDB
645 Candida Genome Candida albicans genome database http://www.candidagenome.org/
441 CYGD MIPS Comprehensive yeast genome database http://mips.gsf.de/proj/yeast
483 Génolevures A comparison of S.cerevisiae and 14 other yeast species http://cbi.labri.fr/Genolevures
730 PROPHECY Profiling of phenotypic characteristics in yeast http://prophecy.lundberg.gu.se/
576 SCMD Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants http://yeast.gi.k.u-tokyo.ac.jp/
577 SCPD Saccharomyces cerevisiae promoter database http://cgsigma.cshl.org/jian
357 SGD Saccharomyces genome database http://www.yeastgenome.org/
25 TRIPLES Transposon-insertion phenotypes, localization and expression in Saccharomyces http://ygac.med.yale.edu/triples/
306 YDPM Yeast deletion project and mitochondria database http://www-deletion.stanford.edu/YDPM/YDPM_index.html
342 Yeast Intron Database Ares lab database of splicesomal introns in S.cerevisiae http://www.cse.ucsc.edu/research/compbio/yeast_introns.html
254 Yeast snoRNA Database Yeast small nucleolar RNAs http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
307 yMGV Yeast microarray global viewer http://www.transcriptome.ens.fr/ymgv/
763 YRC PDR Yeast resource center public data repository http://www.yeastrc.org/pdr/
5.3.4.2. Other fungi
425 CADRE Central Aspergillus data repository http://www.cadre.man.ac.uk/
435 COGEME Phytopathogenic fungi and oomycete EST database http://cogeme.ex.ac.uk/
533 MNCDB MIPS Neurospora crassa database http://mips.gsf.de/proj/neurospora/
708 OGD Oomycete Genomics Database: ESTs and annotation http://www.oomycete.net/
98 Phytophthora Functional Genomics Database ESTs and expression data from P.infestans and P.sojae http://www.pfgd.org/pfgd/
5.3.5. Invertebrates
5.3.5.1. Caenorhabditis elegans
430 C.elegans Project Genome sequencing data at the Sanger Institute http://www.sanger.ac.uk/Projects/C_elegans
238 Intronerator Introns and splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
570 RNAiDB RNAi phenotypic analysis of C.elegans genes http://www.rnai.org/
100 WILMA C.elegans annotation database http://www.came.sbg.ac.at/wilma/
304 WorfDB C.elegans ORFeome http://worfdb.dfci.harvard.edu/
51 WormBase Data repository for C.elegans and C.briggsae: curated genome annotation, genetic and physical maps, pathways http://www.wormbase.org/
5.3.5.2. Drosophila melanogaster
71 FlyBase Drosophila sequences and genomic information http://flybase.bio.indiana.edu/
767 FlyBrain Database of the Drosophila nervous system http://flybrain.neurobio.arizona.edu/
670 FlyMine Integration of insect genomic and proteomic data http://www.flymine.org/
467 FlyTrap Drosophila mutants created using GFP protein trap strategy http://flytrap.med.yale.edu/
471 GadFly Genome annotation database of Drosophila http://www.fruitfly.org/
677 GeniSys Enhancer- and promoter-inserted mutants of Drosophila http://genisys.kaist.ac.kr:8080/
774 DPDB Drosophila polymorphism database http://dpdb.uab.es/
449 Drosophila microarray project Data and tools for Drosophila gene expression studies http://www.flyarrays.com/fruitfly
509 InterActive Fly Drosophila genes and their roles in development http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm
5.3.5.3. Other invertebrates
410 AppaDB A database on the nematode Pristionchus pacificus http://appadb.eb.tuebingen.mpg.de/
643 BeetleBase Genome database of the beetle Tribolium castaneum http://www.bioinformatics.ksu.edu/BeetleBase/
649 Ciliate IES-MDS Db Macro- and micronuclear genes in spirotrichous ciliates http://oxytricha.princeton.edu/dimorphism/database.htm
434 CnidBase Cnidarian evolution and gene expression database http://cnidbase.bu.edu/
543 Nematode.net Parasitic nematode sequencing project http://nematode.net/
544 NEMBASE Nematode sequence and functional data database http://www.nematodes.org/
726 PPNEMA Plant-parasitic nematode rRNAs http://bighost.area.ba.cnr.it/PPNEMA/
743 SilkDB Silkworm Bombyx mori ESTs, mutants, photographs http://www.ab.a.u-tokyo.ac.jp/genome/
744 SilkSatDb A microsatellite database of the silkworm Bombyx mori http://www.cdfd.org.in/silksatdb/
747 SpodoBase Genomics of the butterfly Spodoptera frugiperda http://bioweb.ensam.inra.fr/spodobase/
6. Metabolic Enzymes and Pathways; Signaling Pathways
6.1. Enzymes and Enzyme Nomenclature
421 BRENDA Enzyme names and biochemical properties http://www.brenda.uni-koeln.de/
109 ENZYME Enzyme nomenclature and properties http://www.expasy.org/enzyme
459 Enzyme Nomenclature IUBMB Nomenclature Committee recommendations http://www.chem.qmw.ac.uk/iubmb/enzyme
613 EzCatDB Enzyme Catalytic Mechanism Database http://mbs.cbrc.jp/EzCatDB/
508 IntEnz Integrated enzyme database and enzyme nomenclature http://www.ebi.ac.uk/intenz
716 PDBrtf Representation of target families of enzymes in PDB http://cgl.imim.es/pdbrtf/
758 SCOPEC Mapping of catalytic function to domain structure http://www.enzome.com/databases/scopec.php
6.2. Metabolic Pathways
644 BioSilico Integrated access to various metabolic databases http://biosilico.kaist.ac.kr/
112 KEGG Pathway Metabolic and regulatory pathways in complete genomes http://www.genome.jp/kegg/pathway.html
114 MetaCyc Metabolic pathways and enzymes from various organisms http://metacyc.org/
115 PathDB Biochemical pathways, compounds and metabolism http://www.ncgr.org/pathdb
117 UM-BBD University of Minnesota biocatalysis and biodegradation database http://umbbd.ahc.umn.edu/
6.3. Intermolecular Interactions and Signaling Pathways
633 3DID 3D interacting domains: domain–domain interactions in proteins with known 3D structures http://3did.embl.de/
405 aMAZE A system for the annotation, management, and analysis of biochemical and signalling pathway networks http://www.amaze.ulb.ac.be/
103 BIND Biomolecular interaction network database http://www.bind.ca/
419 BioCarta Online maps of metabolic and signaling pathways http://www.biocarta.com/genes/allPathways.asp
422 BRITE Biomolecular relations in information transmission and expression, part of KEGG
659 DDIB Database of domain interactions and binding http://www.ddib.org/
104 DIP Database of interacting proteins: experimentally determined protein–protein interactions http://dip.doe-mbi.ucla.edu/
105 DRC Database of ribosomal crosslinks http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc
329 GeneNet Database on gene network components http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet
664 hp-DPI Database of protein interactions in Helicobacter pylori http://dpi.nhri.org.tw/hp/
688 HPID Human protein interaction database http://www.hpid.org/
507 IntAct project Protein–protein interaction data http://www.ebi.ac.uk/intact
770 Inter-Chain Beta-Sheets Protein–protein interactions mediated by interchain beta-sheet formation http://www.igb.uci.edu/servers/icbs/
510 InterDom Putative protein domain interactions http://interdom.lit.org.sg/
718 PDZBase Protein–protein interactions involving PDZ domains http://icb.med.cornell.edu/services/pdz/start
749 Protein-protein interfaces Interacting residues in protein–protein interfaces in PDB http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
773 PINdb Proteins interacting in nucleus (human and yeast) http://pin.mskcc.org/
748 POINT Prediction of human protein–protein interactome http://point.nchc.org.tw/
616 PSIbase Interaction of proteins with known 3D structures http://psimap.kaist.ac.kr/
612 Reactome A knowledgebase of biological pathways http://www.reactome.org/
571 ROSPath Reactive oxygen species (ROS) signaling pathway http://rospath.ewha.ac.kr/
395 STCDB Signal transductions classification database http://bibiserv.techfak.uni-bielefeld.de/stcdb/
582 STRING Predicted functional associations between proteins http://string.embl.de/
341 TRANSPATH Gene regulatory networks and microarray analysis http://www.biobase.de/pages/products/databases.html
7. Human and other Vertebrate Genomes
7.1. Model organisms, comparative genomics
63 ACeDB C.elegans, S.pombe and human genomic information http://www.acedb.org/
26 AllGenes Human and mouse gene, transcript and protein annotation http://www.allgenes.org/
65 ArkDB Genome databases for farm and other animals http://www.thearkdb.org/
647 ChickVD Sequence variation in the chicken genome http://chicken.genomics.org.cn/
286 Cre Transgenic Database Cre transgenic mouse lines with links to publications http://www.mshri.on.ca/nagy/
660 DED Database of evolutionary distances http://warta.bio.psu.edu/DED/
27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/
465 FANTOM Functional annotation of mouse full-length cDNA clones http://fantom2.gsc.riken.go.jp/
468 FREP Functional repeats in mouse cDNAs http://facts.gsc.riken.go.jp/FREP/
673 GALA Genomic alignment, annotation and experimental results http://gala.cse.psu.edu/
347 GenetPig Genes controlling economic traits in pig http://www.infobiogen.fr/services/Genetpig
605 HomoloGene Automatically detected homologous genes in complete eukaryotic genomes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
690 Inparanoid A database of eukaryotic orthologs http://inparanoid.cgb.ki.se/
696 IPI International protein index: non-redundant sets of human, mouse and rat proteins http://www.ebi.ac.uk/IPI
777 KaryotypeDB Karyotype and chromosome information for animal and plant species http://www.nenno.it/karyotypedb/
400 KOG Eukaryotic orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi
87 Mouse Genome Informatics Formerly mouse genome database http://www.informatics.jax.org/
540 MTID Mouse transposon insertion database http://mouse.ccgb.umn.edu/transposon/
703 NegProt Negative Proteome: a tool for comparison of complete proteomes http://superfly.ucsd.edu/negprot
556 PEDE Pig EST data explorer: full-length cDNAs and ESTs http://pede.gene.staff.or.jp/
665 PhenomicDB Comparison of phenotypes of orthologous genes in human and model organisms http://www.phenomicdb.de/
724 Polymorphix A database of sequence polymorphisms http://pbil.univ-lyon1.fr/polymorphix/query.php
93 Rat Genome Database Rat genetic and genomic data http://rgd.mcw.edu/
625 RatMap Rat genome tools and data http://ratmap.org/
751 TAED The adaptive evolution database: a phylogeny-based tool for comparative genomics http://www.bioinfo.no/tools/TAED
5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml
6 UniGene Unified clusters of ESTs and full-length mRNA sequences http://www.ncbi.nlm.nih.gov/UniGene/
319 UniSTS Unified view of sequence tagged sites with mapping data http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
783 VEGA Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences http://vega.sanger.ac.uk/
101 ZFIN Zebrafish information network http://zfin.org/
7.2. Human genome databases, maps and viewers
27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/
404 AluGene Complete Alu map in the human genome http://alugene.tau.ac.il/
349 CroW 21 Human chromosome 21 database http://bioinfo.weizmann.ac.il/crow21/
55 GB4-RH Genebridge4 human radiation hybrid maps http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml
56 GDB Human genes and genomic maps http://www.gdb.org/
57 GenAtlas Human genes, markers and phenotypes http://www.genatlas.org/
350 GeneCards Integrated database of human genes, maps, proteins and diseases http://bioinfo.weizmann.ac.il/cards/
348 GeneLoc Gene location database (formerly UDB—Unified database for human genome mapping) http://genecards.weizmann.ac.il/geneloc/
327 GeneNest Gene indices of human, mouse, zebrafish, etc. http://genenest.molgen.mpg.de/
59 GenMapDB Mapped human BAC clones http://genomics.med.upenn.edu/genmapdb
35 Gene Resource Locator Alignment of ESTs with finished human sequence http://grl.gi.k.u-tokyo.ac.jp/
324 HOWDY Human organized whole genome database http://www-alis.tokyo.jst.go.jp/HOWDY/
60 HuGeMap Human genome genetic and physical map data http://www.infobiogen.fr/services/Hugemap
77 Human BAC Ends Non-redundant human BAC end sequences http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
597 Human Genome Segmental Duplication Database Segmental duplications in the human genome http://projects.tcag.ca/humandup
61 IXDB Physical maps of human chromosome X http://ixdb.mpimg-berlin-dahlem.mpg.de/
697 L1Base Functional annotation and prediction of LINE-1 elements http://line1.molgen.mpg.de/
54 Map Viewer Display of genomic information by chromosomal position http://www.ncbi.nlm.nih.gov/mapview/
600 MGC Mammalian genome collection: full-length ORFs for human, mouse and rat genes http://mgc.nci.nih.gov/
391 NCBI RefSeq Non-redundant collection of naturally occurring biological molecules http://www.ncbi.nlm.nih.gov/RefSeq/
553 ParaDB Paralogy mapping in human genomes http://abi.marseille.inserm.fr/paradb/
62 RHdb Radiation hybrid map data http://www.ebi.ac.uk/RHdb
592 SKY/M-FISH and CGH Fluorescent images of chromosomes and cytogenetic data http://www.ncbi.nlm.nih.gov/sky/
4 STACK Sequence tag alignment and consensus knowledgebase http://www.sanbi.ac.za/Dbases.html
596 The Chromosome 7 Annotation Project A comprehensive description of human chromosome 7 http://www.chr7.org/
684 TRBase Tandem repeats in the human genome http://bioinfo.ex.ac.uk/trbase
316 UCSC Genome Browser Genome assemblies and annotation http://genome.ucsc.edu/
7.3. Human proteins
685 H-InvDB Full-length human cDNA clones http://www.h-invitational.jp/
499 HPMR Human plasma membrane receptome: sequences, literature and expression data http://receptome.stanford.edu/
500 HPRD Human protein reference database: domain architecture, post-translational modifications and disease association http://www.hprd.org/
37 HUNT Human novel transcripts: annotated full-length cDNAs http://www.hri.co.jp/HUNT
171 HUGE Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences http://www.kazusa.or.jp/huge
522 LIFEdb Localization, interaction and functions of human proteins http://www.dkfz.de/LIFEdb
312 trome, trEST and trGEN: Databases of predicted human protein sequences ftp://ftp.isrec.isb-sib.ch/pub/databases/
8. Human Genes and Diseases
8.1. General Databases
661 DG-CST Disease gene conserved sequence tags http://143.225.208.11/cst3/
683 HCAD Human chromosome aberration database: chromosomal breakpoints and affected genes http://www.pdg.cnb.uam.es/UniPub/HCAD/
8 Homophila Drosophila homologs of human disease genes to http://superfly.ucsd.edu/homophila/
548 OMIA Online Mendelian inheritance in animals: a catalog of animal genetic and genomic disorders http://www.angis.org.au/omia
143 OMIM Online Mendelian inheritance in man: a catalog of human genetic and genomic disorders http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
550 ORFDB Collection of ORFs that are sold by Invitrogen http://orf.invitrogen.com/
554 PathBase European mutant mice histopathology database: images http://www.pathbase.net/
146 PMD Compilation of protein mutant data http://pmd.ddbj.nig.ac.jp/
358 SOURCE Functional genomics resource for human, mouse and rat http://source.stanford.edu/
8.2. Human Mutations Databases
8.2.1. General polymorphism databases
119 ALFRED Allele frequencies and DNA polymorphisms http://alfred.med.yale.edu/
416 BayGenomics Genes relevant to cardiovascular and pulmonary disease http://baygenomics.ucsf.edu/
654 Cypriot national mutation database Disease mutations in the Cypriot population http://www.goldenhelix.org/cypriot/
655 Database of Genomic Variants Human genomic variants: frequency, segmental duplications and genome assembly gaps http://projects.tcag.ca/variation/
595 dbQSNP Quantification of SNP allele frequencies database http://qsnp.gen.kyushu-u.ac.jp/
127 dbSNP Database of single nucleotide polymorphisms http://www.ncbi.nlm.nih.gov/SNP/
669 FESD Functional element SNPs database: SNPs located within promoters, UTRs, etc., of human genes http://combio.kribb.re.kr/ksnp/resd/
496 HGVS Databases A compilation of human mutation databases http://www.hgvs.org/
131 HGVbase Human genome variation database: curated human polymorphisms http://hgvbase.cgb.ki.se/
133 HGMD Human gene mutation database http://www.hgmd.org/
367 IPD Immuno polymorphism database http://www.ebi.ac.uk/ipd
517 JSNP Japanese SNP database http://snp.ims.u-tokyo.ac.jp/
45 rSNP Guide SNPs in regulatory gene regions http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
344 SNP Consortium database SNP Consortium data http://snp.cshl.org/
626 SNPeffect Phenotypic effects of human coding SNPs http://snpeffect.vib.be/
590 TopoSNP Topographic database of non-synonymous SNPs http://gila.bioengr.uic.edu/snp/toposnp
755 TPMD Taiwan polymorphic microsatellite marker database http://tpmd.nhri.org.tw/
8.2.2. Cancer
122 Atlas of Genetics and Cytogenetics in Oncology and Haematology Cancer-related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases http://www.infobiogen.fr/services/chromcancer/
593 Cancer Chromosomes Cytogenetic, clinical and reference information on cancer-related aberrations http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes
431 CGED Cancer gene expression database http://love2.aist-nara.ac.jp/CGED
651 COSMIC Catalogue of somatic mutations in cancer: sequence data, samples and publications http://www.sanger.ac.uk/perl/CGP/cosmic
126 Germline p53 Mutations Mutations in human tumor and cell line p53 gene http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm
362 IARC TP53 Database Human TP53 somatic and germline mutations http://www.iarc.fr/p53/
152 MTB Mouse tumor biology database: tumor types, genes, classification, incidence, pathology http://tumor.informatics.jax.org/
709 OncoMine Cancer microarray data by gene or cancer type http://www.oncomine.org/
153 Oral Cancer Gene Database Cellular and molecular data for genes involved in oral cancer http://www.tumor-gene.org/Oral/oral.html
148 RB1 Gene Mutation DB Mutations in the human retinoblastoma (RB1) gene http://www.d-lohmann.de/Rb/
574 RTCGD Mouse retroviral tagged cancer gene database http://rtcgd.ncifcrf.gov/
579 SNP500Cancer Re-sequenced SNPs from 102 reference samples http://snp500cancer.nci.nih.gov/
149 SV40 Large T-Antigen Mutants Mutations in SV40 large tumor antigen gene http://supernova.bio.pitt.edu/pipaslab/
155 Tumor Gene Family Databases Cellular, molecular and biological data about genes involved in various cancers http://www.tumor-gene.org/tgdf.html
8.2.3. Gene-, system- or disease-specific
768 ALPSbase Autoimmune lymphoproliferative syndrome database http://research.nhgri.nih.gov/alps/
120 Androgen Receptor Gene Mutations Database Mutations in the androgen receptor gene http://www.mcgill.ca/androgendb/
123 BTKbase Mutation registry for X-linked agammaglobulinemia http://bioinf.uta.fi/BTKbase/
594 CarpeDB Comprehensive database on the genetics of epilepsy http://www.carpedb.ua.edu/
124 CASRDB Calcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism http://www.casrdb.mcgill.ca/
125 Cytokine Gene Polymorphism in Human Disease Cytokine gene polymorphism literature database http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm
137 Collagen Mutation Database Human type I and type III collagen gene mutations http://www.le.ac.uk/genetics/collagen/
460 ERGDB Estrogen responsive genes database http://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/
164 FUNPEP Low-complexity peptides capable of forming amyloid plaque http://www.cmbi.kun.nl/swift/FUNPEP/gergo/
363 GOLD.db Genomics of lipid-associated disorders database http://gold.tugraz.at/
129 GRAP Mutants of G-protein coupled receptors of family A http://tinygrap.uit.no/GRAP/
130 HaemB Factor IX gene mutations, insertions and deletions http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html
491 HbVar Human hemoglobin variants and thalassemias http://globin.cse.psu.edu/globin/hbvar
680 HAGR Human ageing genomic resources: genes related to ageing in humans and model organisms http://genomics.senescence.info/
134 Human p53/hprt, rodent lacI/lacZ databases Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations http://www.ibiblio.org/dnam/mainpage.html
135 Human PAX2 Allelic Variant Database Mutations in human PAX2 gene http://pax2.hgu.mrc.ac.uk/
136 Human PAX6 Allelic Variant Database Mutations in human PAX6 gene http://pax6.hgu.mrc.ac.uk/
506 INFEVERS Hereditary inflammatory disorder and familial mediterranean fever mutation data http://fmf.igh.cnrs.fr/infevers
139 KinMutBase Disease-causing protein kinase mutations http://www.uta.fi/imt/bioinfo/KinMutBase/
523 Lowe Syndrome Mutation Database Mutations causing Lowe oculocerebrorenal syndrome http://research.nhgri.nih.gov/lowe/
142 NCL Mutation Database Polymorphisms in neuronal ceroid lipofuscinoses genes http://www.ucl.ac.uk/ncl/
144 PAHdb Mutations at the phenylalanine hydroxylase locus http://www.mcgill.ca/pahdb/
559 PGDB Prostate and prostatic diseases gene database http://www.ucsf.edu/pgdb/
145 PHEXdb PHEX mutations causing X-linked hypophosphatemia http://www.phexdb.mcgill.ca/
147 PTCH1 Mutation Database Mutations and SNPs found in PTCH1 gene http://www.cybergene.se/PTCH/ptchbase.html
SCAdb Spinocerebellar ataxia candidate gene database http://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map
632 T1Dbase A resource for type 1 diabetes research http://t1dbase.org/
752 The Autism Chromosome Rearrangement Database Curated collection of genomic features related to autism http://projects.tcag.ca/autism
753 The Lafora Database Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy http://projects.tcag.ca/lafora/
9. Microarray Data and other Gene Expression Databases
634 5'SAGE 5'-end serial analysis of gene expression http://5sage.gi.k.u-tokyo.ac.jp/
338 ArrayExpress Public collection of microarray gene expression data http://www.ebi.ac.uk/arrayexpress
11 Axeldb Gene expression in Xenopus laevis http://www.dkfz-heidelberg.de/abt0135/axeldb.htm
12 BodyMap Human and mouse gene expression data http://bodymap.ims.u-tokyo.ac.jp/
417 BGED Brain gene expression database http://love2.aist-nara.ac.jp/BGED
432 CleanEx Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons http://www.cleanex.isb-sib.ch/
657 dbERGEII Database of experimental results on gene expression: genomic alignment, annotation and experimental data http://dberge.cse.psu.edu/menu.html
454 EICO DB Expression-based imprint candidate organiser: a database for discovery of novel imprinted genes http://fantom2.gsc.riken.jp/EICODB/
455 emap Atlas Edinburgh mouse atlas: a digital atlas of mouse embryo development and spatially mapped gene expression http://genex.hgu.mrc.ac.uk/
13 EPConDB Endocrine pancreas consortium database http://www.cbil.upenn.edu/EPConDB
110 EpoDB Genes expressed during human erythropoiesis http://www.cbil.upenn.edu/EpoDB/
14 FlyView Drosophila development and genetics http://pbio07.uni-muenster.de/
326 GeneAnnot Revised annotation of Affymetrix human gene probe sets http://genecards.weizmann.ac.il/geneannot/
325 GeneNote Human genes expression profiles in healthy tissues http://genecards.weizmann.ac.il/genenote/
330 GenePaint Gene expression patterns in the mouse http://www.genepaint.org/Frameset.html
676 GeneTide A transcriptome-focused member of the GeneCards suite http://genecards.weizmann.ac.il/genetide/
481 GeneTrap Expression patterns in an embryonic stem library of gene trap insertions http://www.cmhd.ca/sub/genetrap.asp
603 GEO Gene expression omnibus: gene expression profiles http://www.ncbi.nlm.nih.gov/geo/
485 GermOnline Gene expression in mitotic and meiotic cell cycle http://www.germonline.org/
15 GXD Mouse gene expression database http://www.informatics.jax.org/menus/expression_menu.shtml
681 H-ANGEL Human anatomic gene expression library http://www.jbirc.aist.go.jp/hinv/index.jsp
493 HemBase Genes expressed in differentiating human erythroid cells http://hembase.niddk.nih.gov/
23 HugeIndex Expression levels of human genes in normal tissues http://hugeindex.org/
17 Kidney Development Database Kidney development and gene expression http://golgi.ana.ed.ac.uk/kidhome.html
778 LOLA List of lists annotated: a comparison of gene sets identified in different microarray experiments http://www.lola.gwu.edu/
18 MAGEST Ascidian (Halocynthia roretzi) gene expression patterns
699 MAMEP Molecular anatomy of the mouse embryo project: gene expression data on mouse embryos http://mamep.molgen.mpg.de/
339 MEPD Medaka (freshwater fish Oryzias latipes) gene expression pattern database http://www.embl.de/mepd/
19 MethDB DNA methylation data, patterns and profiles http://www.methdb.de/
537 Mouse SAGE SAGE libraries from various mouse tissues and cell lines http://mouse.biomed.cas.cz/sage
541 NASCarrays Nottingham Arabidopsis Stock Centre microarray database http://affymetrix.arabidopsis.info/
545 NetAffx Public Affymetrix probesets and annotations http://www.affymetrix.com/
711 Osteo-Promoter Database Genes in osteogenic proliferation and differentiation http://www.opd.tau.ac.il/
154 PEDB Prostate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries http://www.pedb.org/
558 PEPR Public expression profiling resource: expression profiles in a variety of diseases and conditions http://microarray.cnmcresearch.org/pgadatatable.asp
21 RECODE Genes using programmed translational recoding in their expression http://recode.genetics.utah.edu/
568 RefExA Reference database for human gene expression analysis http://www.lsbm.org/db/index_e.html
739 rOGED Rat ovarian gene expression database http://web5.mccs.uky.edu/kolab/rogedendo.aspx
712 SAGEmap NCBI's resource for SAGE data from various organisms http://www.ncbi.nlm.nih.gov/SAGE
742 SIEGE Smoking Induced Epithelial Gene Expression http://pulm.bumc.bu.edu/siegeDB
22 Stanford Microarray Database Raw and normalized data from microarray experiments http://genome-www.stanford.edu/microarray
24 Tooth Development Database Gene expression in dental tissue http://bite-it.helsinki.fi/
10. Proteomics Resources
606 2D-PAGE Proteome database system for microbial research http://www.mpiib-berlin.mpg.de/2D-PAGE
731 DynaProt 2D Proteome database of Lactococcus lactis http://www.wzw.tum.de/proteomik/lactis/
222 GelBank 2D gel electrophoresis patterns of proteins from complete microbial genomes http://gelbank.anl.gov/
710 Open Proteomics Database Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium http://bioinformatics.icmb.utexas.edu/OPD/
377 PEP Predictions for entire proteomes: summarized analyses of protein sequences http://cubic.bioc.columbia.edu/pep/
281 RESID Pre-, co- and post-translational protein modifications http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html
225 SWISS-2DPAGE Annotated 2D gel electrophoresis database http://www.expasy.org/ch2d/
11. Other Molecular Biology Databases
11.1. Drugs and drug design
407 ANTIMIC Database of natural antimicrobial peptides http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/
781 AOBase Antisense oligonucleotide selection and design http://www.bio-inf.net/aobase/
408 APD Antimicrobial peptide database http://aps.unmc.edu/AP/main.php
423 BSD Biodegradative strain database: microorganisms that can degrade aromatic and other organic compounds http://bsd.cme.msu.edu/
443 DART Drug adverse reaction target database http://xin.cz3.nus.edu.sg/group/drt/dart.asp
701 MetaRouter Compounds and pathways related to bioremediation http://pdg.cnb.uam.es/MetaRouter/
186 Peptaibol Peptaibol (antibiotic peptide) sequences http://www.cryst.bbk.ac.uk/peptaibol/welcome.html
392 PharmGKB Pharmacogenomics knowledge base: effect of genetic variation on drug responses http://www.pharmgkb.org/
315 TTD Therapeutic target database http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp
11.2. Probes
505 IMGT/PRIMER-DB Immunogenetics oligonucleotide primer database http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl
296 MPDB Synthetic oligonucleotides useful as primers or probes http://www.biotech.ist.unige.it/interlab/mpdb.html
728 PrimerPCR PCR primers for eukaryotic and prokaryotic genes http://bioinfo.ebc.ee/PrimerStudio/
390 probeBase rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information http://www.microbial-ecology.net/probebase
736 QPPD Quantitative PCR Primer Database for human and mouse http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp
356 RTPrimerDB Real-time PCR primer and probe sequences http://medgen.ugent.be/rtprimerdb/
11.3. Unclassified databases
298 PubMed Citations and abstracts of biomedical literature http://pubmed.gov/
256 BioImage Database of multidimensional biological images http://www.bioimage.org/
12. Organelle Databases
74 GOBASE Organelle genome database http://megasun.bch.umontreal.ca/gobase/
547 OGRe Organelle genome retrieval system http://ogre.mcmaster.ca/
601 Organelle genomes NCBI's organelle genome resource http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
722 PLprot Arabidopsis thaliana chloroplast protein database http://www.pb.ipw.biol.ethz.ch/proteomics
713 Organelle DB Organelle proteins and subcellular structures http://organelledb.lsi.umich.edu/
12.1. Mitochondrial Genes and Proteins
637 AMPDB Arabidopsis mitochondrial protein database http://www.mitoz.bcs.uwa.edu.au/AMPDB/
686 HMPD Human mitochondrial protein database http://bioinfo.nist.gov:8080/examples/servlets/index.html
38 HvrBase Primate mitochondrial DNA control region sequences http://www.hvrbase.org/
64 Mitochondriome Metazoan mitochondrial genes http://www.ba.itb.cnr.it/mitochondriome
83 MitoDat Mitochondrial proteins (predominantly human) http://www-lecb.ncifcrf.gov/mitoDat/
226 MitoDrome Nuclear-encoded mitochondrial proteins of Drosophila http://www2.ba.itb.cnr.it/MitoDrome/
84 MitoMap Human mitochondrial genome http://www.mitomap.org/
85 MitoNuc Nuclear genes coding for mitochondrial proteins http://www2.ba.itb.cnr.it/MitoNuc/
86 MITOP2 Mitochondrial proteins, genes and diseases http://ihg.gsf.de/mitop2/start.jsp
531 MitoPD Yeast mitochondrial protein database http://bmerc-www.bu.edu/mito
532 MitoProteome Experimentally described human mitochondrial proteins http://www.mitoproteome.org/
538 MPIMP Mitochondrial protein import machinery of plants http://millar3.biochem.uwa.edu.au/~lister/index.html
241 PLMItRNA Plant mitochondrial tRNA http://bighost.area.ba.cnr.it/PLMItRNA/
13. Plant Databases
13.1. General plant databases
599 BarleyBase Expression profiling of plant genomes http://www.barleybase.org/
624 CR-EST Crop ESTs: barley, pea, wheat and potato http://pgrc.ipk-gatersleben.de/cr-est/
67 CropNet Genome mapping in crop plants http://ukcrop.net/
128 FLAGdb++ Integrative database about plant genomes http://genoplante-info.infobiogen.fr/FLAGdb/
351 GénoPlante-Info Plant genomic data from the Génoplante consortium http://genoplante-info.infobiogen.fr/
488 GrainGenes Genes and phenotypes of wheat, barley, rye, triticale, oats http://wheat.pw.usda.gov/ or http://www.graingenes.org/
607 Gramene A resource for comparative grass genomics http://www.gramene.org/
81 Mendel Annotated plant ESTs and STSs http://www.mendel.ac.uk/
581 openSputnik Plant EST clustering and functional annotation http://sputnik.btk.fi/
560 PhytoProt Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot
721 PlantMarkers A database of predicted molecular markers from plants http://markers.btk.fi/
355 PlantGDB Plant genome database: actively transcribed plant genes http://www.plantgdb.org/
189 PLANT-PIs Plant protease inhibitors http://bighost.area.ba.cnr.it/PLANT-PIs
371 PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/
588 TIGR plant repeat database Classification of repetitive sequences in plant genomes http://www.tigr.org/tdb/e2k1/plant.repeats
313 TropGENE DB Genes and genomes of sugarcane, banana, cocoa http://tropgenedb.cirad.fr/
13.2. Arabidopsis thaliana
636 AGNS Arabidopsis GeneNet supplementary: gene expression and phenotypes of mutants and transgens http://emj-pc.ics.uci.edu/mgs/dbases/agns
618 AGRIS Arabidopsis gene regulatory information server: promoters, transcription factors and their target genes http://arabidopsis.med.ohio-state.edu/
780 Arabidopsis MPSS Arabidopsis gene expression detected by massively parallel signature sequencing http://mpss.udel.edu/at/
638 Arabidopsis Nucleolar Protein Database Comparative analysis of human and Arabidopsis nucleolar proteomes http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/proteome_comparison
640 ASRP Arabidopsis thaliana small RNA project http://cgrb.orst.edu/smallRNA/db/
412 ARAMEMNON Arabidopsis thaliana membrane proteins and transporters http://aramemnon.botanik.uni-koeln.de/
765 AthaMap Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana http://www.athamap.de/
427 CATMA Complete Arabidopsis transcriptome microarray http://www.catma.org/
656 DATF Database of Arabidopsis transcription factors http://datf.cbi.pku.edu.cn/
672 GabiPD Central database of the German Plant Genome Project http://gabi.rzpd.de/
675 GeneFarm Expert annotation of Arabidopsis gene and protein families http://genoplante-info.infobiogen.fr/Genefarm/
527 MAtDB MIPS Arabidopsis thaliana database http://mips.gsf.de/proj/thal/db
738 RARGE RIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and microarray data http://rarge.gsc.riken.jp/
578 SeedGenes Genes essential for Arabidopsis development http://www.seedgenes.org/
97 TAIR The Arabidopsis information resource http://www.arabidopsis.org/
627 WAtDB Wageningen Arabidopsis thaliana database: mutants, transgenic lines and natural variants http://www.watdb.nl/
13.3. Rice
418 BGI-RISe Beijing genomics institute rice information system http://rise.genomics.org.cn/
79 INE Integrated rice genome explorer http://rgp.dna.affrc.go.jp/giot/INE.html
353 IRIS International rice information system http://www.iris.irri.org/
536 MOsDB MIPS Oryza sativa database http://mips.gsf.de/proj/plant/jsf/rice/index.jsp
90 Oryzabase Rice genetics and genomics http://www.shigen.nig.ac.jp/rice/oryzabase/
628 Oryza Tag Line database T-DNA insertion mutants of rice http://genoplante-info.infobiogen.fr/OryzaTagLine/
737 RAD Rice annotation database http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html
336 RiceGAAS Rice genome automated annotation system http://ricegaas.dna.affrc.go.jp/
569 Rice PIPELINE Unification tool for rice databases http://cdna01.dna.affrc.go.jp/PIPE
572 Rice proteome database Rice proteome database http://gene64.dna.affrc.go.jp/RPD/main_en.html
13.4. Other plants
610 Brassica ASTRA A database for Brassica genomic research http://hornbill.cspp.latrobe.edu.au/cgi-binpub/index.pl
526 MaizeGDB Maize genetics and genomics database http://www.maizegdb.org/
80 LIS (formerly MGI) Legume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic data http://www.comparative-legumes.org/
539 MtDB Medicago trunculata genome database http://www.medicago.org/MtDB
620 PoMaMo Potato Maps and More: Potato genome data https://gabi.rzpd.de/PoMaMo.html
766 SGMD Soybean genomics and microarray database http://psi081.ba.ars.usda.gov/SGMD/default.htm
14. Immunological Databases
642 BCIpep A database of B-cell epitopes http://bioinformatics.uams.edu/mirror/bcipep/
604 dbMHC Genetic and clinical database of the human MHC http://www.ncbi.nlm.nih.gov/mhc/
150 FIMM Functional molecular immunology data http://research.i2r.a-star.edu.sg/fimm
682 Haptendb Curated database of hapten molecules http://www.imtech.res.in/raghava/haptendb/
779 HLA Ligand/Motif A database and search tool for HLA sequences http://hlaligand.ouhsc.edu/
501 IL2Rgbase X-linked severe combined immunodeficiency mutations http://research.nhgri.nih.gov/scid/
172 IMGT International immunogenetics information system: immunoglobulins, T cell receptors, MHC and RPI http://imgt.cines.fr/
503 IMGT/Gene-DB Vertebrate immunoglobulin and T cell receptor genes http://imgt.cines.fr/cgi-bin/GENElect.jv
173 IMGT/HLA Polymorphism of human MHC and related genes http://www.ebi.ac.uk/imgt/hla/
504 IMGT/LIGM-DB Immunoglobulin, T cell receptor and MHC nucleotide sequences from human and other vertebrates http://imgt.cines.fr/cgi-bin/IMGTlect.jv
16 Interferon Stimulated Gene Database Genes induced by treatment with interferons http://www.lerner.ccf.org/labs/williams/xchip-html.cgi
692 IPD-ESTDAB Immunologically characterized melanoma cell lines http://www.ebi.ac.uk/ipd/estdab/
693 IPD-HPA Immuno polymorphism of human platelet antigens http://www.ebi.ac.uk/ipd/hpa/
694 IPD-KIR Immuno polymorphism of killer-cell Ig-like receptors http://www.ebi.ac.uk/ipd/kir/
691 IPD-MHC Sequences of the major histocompatibility complex http://www.ebi.ac.uk/ipd/mhc/
361 JenPep Quantitative binding data for immunological protein–peptide interactions http://www.jenner.ac.uk/Jenpep
702 MHCBN A database of MHC binding and non-binding peptides http://www.imtech.res.in/raghava/mhcbn/
181 MHCPEP MHC-binding peptides http://wehih.wehi.edu.au/mhcpep/
107 MPID MHC—peptide interaction database http://surya.bic.nus.edu.sg/mpid
621 VBASE2 Variable genes from the Ig loci of human and mouse http://www.vbase2.org/

a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.