Molecular Biology Databases


Molecular Biology for labs

.


Sequencing Data

Molecular Biology Database Collections


No.b
Database name
Full name and/or description
URL
1. Nucleotide Sequence Databases
1.1. International Nucleotide Sequence Database Collaboration
1DDBJ—DNA Data Bank of JapanAll known nucleotide and protein sequenceshttp://www.ddbj.nig.ac.jp/
2EMBL Nucleotide Sequence DatabaseAll known nucleotide and protein sequenceshttp://www.ebi.ac.uk/embl.html
3GenBank®All known nucleotide and protein sequenceshttp://www.ncbi.nlm.nih.gov/Entrez
1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
403ACLAMEA classification of genetic mobile elementshttp://aclame.ulb.ac.be/
30CUTGCodon usage tabulated from GenBankhttp://www.kazusa.or.jp/codon/
480Genetic CodesGenetic codes in various organisms and organelleshttp://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
668Entrez GeneGene-centered information at NCBIhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
495HERVdHuman endogenous retrovirus databasehttp://herv.img.cas.cz/
687HoppsigenHuman and mouse homologous processed pseudogeneshttp://pbil.univ-lyon1.fr/databases/hoppsigen.html
294Imprinted Gene CatalogueImprinted genes and parent-of-origin effects in animalshttp://www.otago.ac.nz/IGC
512IslanderPathogenicity islands and prophages in bacterial genomeshttp://www.indiana.edu/~islander
343MICdbProkaryotic microsatelliteshttp://www.cdfd.org.in/micas
707NPRDNucleosome positioning region databasehttp://srs6.bionet.nsc.ru/srs6/
47STRBaseShort tandem DNA repeats databasehttp://www.cstl.nist.gov/div831/strbase/
5TIGR Gene IndicesOrganism-specific databases of EST and gene sequenceshttp://www.tigr.org/tdb/tgi.shtml
48TranstermCodon usage, start and stop signalshttp://uther.otago.ac.nz/Transterm.html
6UniGeneNon-redundant set of eukaryotic gene-oriented clustershttp://www.ncbi.nlm.nih.gov/UniGene/
320UniVecVector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contaminationhttp://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
302VectorDBCharacterization and classification of nucleic acid vectorshttp://genome-www2.stanford.edu/vectordb/
305XproEukaryotic protein-encoding DNA sequences, both intron-containing and intron-less geneshttp://origin.bic.nus.edu.sg/xpro/
1.2.2. Gene structure, introns and exons, splice sites
414ASAPAlternative spliced isoformshttp://www.bioinformatics.ucla.edu/ASAP
28ASDAlternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdbhttp://www.ebi.ac.uk/asd
10ASDBAlternative splicing database: protein products and expression patterns of alternatively spliced geneshttp://hazelton.lbl.gov/~teplitski/alt
639ASHESdbAlternatively spliced human genes by exon skipping databasehttp://sege.ntu.edu.sg/wester/ashes/
450EASEDExtended alternatively spliced EST databasehttp://eased.bioinf.mdc-berlin.de/
667ECgeneGenome annotation for alternative splicinghttp://genome.ewha.ac.kr/ECgene/
631EDASEST-derived alternative splicing databasehttp://www.ig-msk.ru:8005/EDAS/
34ExIntExon–intron structure of eukaryotic geneshttp://sege.ntu.edu.sg/wester/exint/
36HS3DHomo sapiens splice sites datasethttp://www.sci.unisannio.it/docenti/rampone/
238IntroneratorAlternative splicing in C.elegans and C.briggsaehttp://www.cse.ucsc.edu/~kent/intronerator/
46SpliceDBCanonical and non-canonical mammalian splice siteshttp://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb
746SpliceInfoModes of alternative splicing in human genomehttp://140.115.50.96/SpliceInfo/
580SpliceNestA tool for visualizing splicing of genes from EST datahttp://splicenest.molgen.mpg.de/
1.2.3. Transcriptional regulator sites and transcription factors
231ACTIVITYFunctional DNA/RNA site activityhttp://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
31DBTBSBacillus subtilis promoters and transcription factorshttp://dbtbs.hgc.jp/
663DoOPDatabase of orthologous promoters: chordates and plantshttp://doop.abc.hu/
106DPInteractBinding sites for E.coli DNA-binding proteinshttp://arep.med.harvard.edu/dpinteract
33EPDEukaryotic promoter databasehttp://www.epd.isb-sib.ch/
494HemoPDBHematopoietic promoter database: transcriptional regulation in hematopoiesishttp://bioinformatics.med.ohio-state.edu/HemoPDB
516JASPARPSSMs for transcription factor DNA-binding siteshttp://jaspar.cgb.ki.se/
700MAPPERPutative transcription factor binding sites in various genomeshttp://bio.chip.org/mapper
40PLACEPlant cis-acting regulatory DNA elementshttp://www.dna.affrc.go.jp/htdocs/PLACE
41PlantCAREPlant promoters and cis-acting regulatory elementshttp://intra.psb.ugent.be:8080/PlantCARE/
563PlantPromPlant promoter sequences for RNA polymerase IIhttp://mendel.cs.rhul.ac.uk/
566PRODORICProkaryotic database of gene regulation networkshttp://prodoric.tu-bs.de/
42PromECE.coli promoters with experimentally identified transcriptional start siteshttp://bioinfo.md.huji.ac.il/marg/promec
246SELEX_DBDNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichmenthttp://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
227TESSTranscription element search systemhttp://www.cbil.upenn.edu/tess
756TRACTOR dbTranscription factors in gamma-proteobacteria databasehttp://www.tractor.lncc.br/
345TRANSCompelComposite regulatory elements affecting gene transcription in eukaryoteshttp://www.gene-regulation.com/pub/databases.html#transcompel
340TRANSFACTranscription factors and binding siteshttp://transfac.gbf.de/TRANSFAC/index.html
757TREDTranscriptional regulatory element databasehttp://rulai.cshl.edu/tred
49TRRDTranscription regulatory regions of eukaryotic geneshttp://www.bionet.nsc.ru/trrd/
2. RNA sequence databases
22916S and 23S rRNA Mutation Database16S and 23S ribosomal RNA mutationshttp://www.fandm.edu/Departments/Biology/Databases/RNA.html
2305S rRNA Database5S rRNA sequenceshttp://biobases.ibch.poznan.pl/5SData/
411Aptamer databaseSmall RNA/DNA molecules binding nucleic acids, proteinshttp://aptamer.icmb.utexas.edu/
232AREDAU-rich element-containing mRNA databasehttp://rc.kfshrc.edu.sa/ared
378Mobile group II intronsA database of group II introns, self-splicing catalytic RNAshttp://www.fp.ucalgary.ca/group2introns/
463European rRNA databaseAll complete or nearly complete rRNA sequenceshttp://www.psb.ugent.be/rRNA/
490GtRDBGenomic tRNA databasehttp://rna.wustl.edu/GtRDB
236Guide RNA DatabaseRNA editing in various kinetoplastid specieshttp://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
76HIV Sequence DatabaseHIV RNA sequenceshttp://hiv-web.lanl.gov/
689HuSiDaHuman siRNA databasehttp://itb1.biologie.hu-berlin.de/~nebulus/sirna/
237HyPaLibHybrid pattern library: structural elements in classes of RNAhttp://bibiserv.techfak.uni-bielefeld.de/HyPa/
379IRESdbInternal ribosome entry site databasehttp://ifr31w3.toulouse.inserm.fr/IRESdatabase/
529microRNA RegistryDatabase of microRNAs (small non-coding RNAs)http://www.sanger.ac.uk/Software/Rfam/mirna/
380NCIRNon-canonical interactions in RNA structureshttp://prion.bchs.uh.edu/bp_type/
381ncRNAs DatabaseNon-coding RNAs with regulatory functionshttp://biobases.ibch.poznan.pl/ncRNA/
705NONCODEA database of non-coding RNAshttp://www.bioinfo.org.cn/NONCODE/index.htm
240PLANTncRNAsPlant non-coding RNAshttp://www.prl.msu.edu/PLANTncRNAs
564Plant snoRNA DBsnoRNA genes in plant specieshttp://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
723PolyA_DBA database of mammalian mRNA polyadenylationhttp://polya.umdnj.edu/polyadb/
242PseudoBaseDatabase of RNA pseudoknotshttp://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
382RfamNon-coding RNA familieshttp://www.sanger.ac.uk/Software/Rfam/
244RISSCRibosomal internal spacer sequence collectionhttp://ulises.umh.es/RISSC
630RNAdbMammalian non-coding RNA databasehttp://ncrna.bioinformatics.com.au/
245RNA Modification DatabaseNaturally modified nucleosides in RNAhttp://medlib.med.utah.edu/RNAmods/
43RRNDBrRNA operon numbers in various prokaryoteshttp://rrndb.cme.msu.edu/
629siRNAdbsiRNA database and search enginehttp://sirna.cgb.ki.se/
247Small RNA DatabaseSmall RNAs from prokaryotes and eukaryoteshttp://mbcr.bcm.tmc.edu/smallRNA
248SRPDBSignal recognition particle databasehttp://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
754SSU rRNA Modification DatabaseModified nucleosides in small subunit rRNAhttp://medstat.med.utah.edu/SSUmods/
383Subviral RNA DatabaseViroids and viroid-like RNAshttp://subviral.med.uottawa.ca/
249tmRNA WebsitetmRNA sequences and alignmentshttp://www.indiana.edu/~tmrna
250tmRDBtmRNA databasehttp://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
251tRNA sequencestRNA viewer and sequence editorhttp://www.uni-bayreuth.de/departments/biochemie/trna/
252UTRdb/UTRsite5'- and 3'-UTRs of eukaryotic mRNAshttp://bighost.area.ba.cnr.it/srs6/
3. Protein sequence databases
3.1. General sequence databases
163EXProtSequences of proteins with experimentally verified functionhttp://www.cmbi.kun.nl/EXProt/
542NCBI Protein databaseAll protein sequences: translated from GenBank and imported from other protein databaseshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
714PA-GOSUBProtein sequences from model organisms, GO assignment and subcellular localizationhttp://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
194PIR-PSDProtein information resource protein sequence database, has been merged into the UniProt knowledgebasehttp://pir.georgetown.edu/
370PIR-NREFPIR's non-redundant reference protein databasehttp://pir.georgetown.edu/pirwww/pirnref.shtml
565PRFProtein research foundation database of peptides: sequences, literature and unnatural amino acidshttp://www.prf.or.jp/en
197Swiss-ProtNow UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebasehttp://www.expasy.org/sprot
198TrEMBLNow UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebasehttp://www.expasy.org/sprot
775UniParcUniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequencehttp://www.uniprot.org/database/archive.shtml
318UniProtUniversal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databaseshttp://www.uniprot.org/
776UniRefUniProt 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
221AAindexPhysicochemical properties of amino acids
729ProNITThermodynamic data on protein–nucleic acid interactionshttp://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
280ProThermThermodynamic data for wild-type and mutant proteinshttp://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
772TECRdbThermodynamics of enzyme-catalyzed reactionshttp://xpdb.nist.gov/enzyme_thermodynamics/
3.3. Protein localization and targeting
444DBSubLocDatabase of protein subcellular localizationhttp://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
375NESbaseNuclear export signals databasehttp://www.cbs.dtu.dk/databases/NESbase
376NLSdbNuclear localization signalshttp://cubic.bioc.columbia.edu/db/NLSdb/
704NMPdbNuclear matrix associated proteins databasehttp://www.rostlab.org/db/NMPdb/
706NOPdbNucleolar proteome databasehttp://www.lamondlab.com/NOPdb/
734PSORTdbProtein subcellular localization in bacteriahttp://db.psort.org/
745SPDSecreted protein databasehttp://spd.cbi.pku.edu.cn/
587THGSTransmembrane helices in genome sequenceshttp://pranag.physics.iisc.ernet.in/thgs/
589TMPDBExperimentally characterized transmembrane topologieshttp://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
3.4. Protein sequence motifs and active sites
374ASCActive sequence collection: biologically active peptideshttp://bioinformatica.isa.cnr.it/ASC/
203BlocksAlignments of conserved regions in protein familieshttp://blocks.fhcrc.org/
440CSACatalytic site atlas: active sites and catalytic residues in enzymes of known 3D structurehttp://www.ebi.ac.uk/thornton-srv/databases/CSA/
438COMeCo-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins)http://www.ebi.ac.uk/come
771CopSComprehensive peptide signature databasehttp://203.195.151.46/copsv2/index.html
666eBLOCKSHighly conserved protein sequence blockshttp://fold.stanford.edu/eblocks/acsearch.html
206eMOTIFProtein sequence motif determination and searcheshttp://motif.stanford.edu/emotif
179Metalloprotein Site DatabaseMetal-binding sites in metalloproteinshttp://metallo.scripps.edu/
209O-GlycBaseO- and C-linked glycosylation sites in proteinshttp://www.cbs.dtu.dk/databases/OGLYCBASE/
717PDBSite3D structure of protein functional siteshttp://srs6.bionet.nsc.ru/srs6/
187Phospho.ELMS/T/Y protein phosphorylation sites (formerly PhosphoBase)http://phospho.elm.eu.org/
193PROMISEProsthetic centers and metal ions in protein active siteshttp://metallo.scripps.edu/PROMISE
215PROSITEBiologically significant protein patterns and profileshttp://www.expasy.org/prosite
732ProTeusSignature sequences at the protein N- and C-terminihttp://www.proteus.cs.huji.ac.il/
3.5. Protein domain databases; protein classification
622ADDAA database of protein domain classificationhttp://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
204CDDConserved domain database, includes protein domains from Pfam, SMART, COG and KOG databaseshttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
205CluSTrClusters of Swiss-Prot+TrEMBL proteinshttp://www.ebi.ac.uk/clustr
671FunShiftFunctional divergence between the subfamilies of a protein domain familyhttp://funshift.cgb.ki.se/
200HitsA database of protein domains and motifshttp://hits.isb-sib.ch/
207InterProIntegrated resource of protein families, domains and functional siteshttp://www.ebi.ac.uk/interpro
208iProClassIntegrated protein classification databasehttp://pir.georgetown.edu/iproclass/
561PIRSFFamily/superfamily classification of whole proteinshttp://pir.georgetown.edu/pirsf/
212PRINTSHierarchical gene family fingerprintshttp://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
210PfamProtein families: multiple sequence alignments and profile hidden Markov models of protein domainshttp://www.sanger.ac.uk/Software/Pfam/
727PRECISEPredicted and consensus interaction sites in enzymeshttp://precise.bu.edu/precisedb/
214ProDomProtein domain familieshttp://www.toulouse.inra.fr/prodom.html
216ProtoMapHierarchical classification of Swiss-Prot proteinshttp://protomap.cornell.edu/
567ProtoNetHierarchical clustering of Swiss-Prot proteinshttp://www.protonet.cs.huji.ac.il/
740S4Structure-based sequence alignments of SCOP superfamilieshttp://compbio.mds.qmw.ac.uk/~james/S4.shtml
217SBASEProtein domain sequences and toolshttp://www.icgeb.org/sbase
218SMARTSimple modular architecture research tool: signalling, extracellular and chromatin-associated protein domainshttp://smart.embl-heidelberg.de/
219SUPFAMGrouping of sequence families into superfamilieshttp://pauling.mbu.iisc.ernet.in/~supfam
220SYSTERSSystematic re-searching and clustering of proteinshttp://systers.molgen.mpg.de/
199TIGRFAMsTIGR protein families adapted for functional annotationhttp://www.tigr.org/TIGRFAMs
3.6. Databases of individual protein families
156AARSDBAminoacyl-tRNA synthetase databasehttp://rose.man.poznan.pl/aars/index.html
308ASPDArtificial selected proteins/peptides databasehttp://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
158BacTregulatorsTranscriptional regulators of AraC and TetR familieshttp://www.bactregulators.org/
364CSDBaseCold shock domain-containing proteinshttp://www.chemie.uni-marburg.de/~csdbase/
653CuticleDBStructural proteins of Arthropod cuticlehttp://bioinformatics.biol.uoa.gr/cuticleDB
658DCCPDatabase of copper-chelating proteinshttp://sdbi.sdut.edu.cn/DCCP/en/index.php
160DExH/D Family DatabaseDEAD-box, DEAH-box and DExH-box proteinshttp://www.helicase.net/dexhd/dbhome.htm
161Endogenous GPCR ListG protein-coupled receptors; expression in cell lineshttp://www.tumor-gene.org/GPCR/gpcr.html
162ESTHEREsterases and other alpha/beta hydrolase enzymeshttp://www.ensam.inra.fr/esther
464EyeSiteFamilies of proteins functioning in the eyehttp://eyesite.cryst.bbk.ac.uk/
166GPCRDBG protein-coupled receptors databasehttp://www.gpcr.org/7tm/
679gpDBG-proteins and their interaction with GPCRshttp://bioinformatics.biol.uoa.gr/gpDB
167Histone DatabaseHistone fold sequences and structureshttp://research.nhgri.nih.gov/histones/
169Homeobox PageHomeobox proteins, classification and evolutionhttp://www.biosci.ki.se/groups/tbu/homeo.html
293Hox-ProHomeobox genes databasehttp://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
170Homeodomain ResourceHomeodomain sequences, structures and related genetic and genomic informationhttp://research.nhgri.nih.gov/homeodomain/
366HORDEHuman olfactory receptor data exploratoriumhttp://bioinfo.weizmann.ac.il/HORDE/
174InBaseInteins (protein splicing elements) database: properties, sequences, bibliographyhttp://www.neb.com/neb/inteins.html
518KinG—Kinases in GenomesS/T/Y-specific protein kinases encoded in complete genomeshttp://hodgkin.mbu.iisc.ernet.in/~king
519KnottinsDatabase of knottins—small proteins with an unusual ‘disulfide through disulfide’ knothttp://knottin.cbs.cnrs.fr/
176LGICdbLigand-gated ion channel subunit sequences databasehttp://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
368Lipase Engineering DatabaseSequence, structure and function of lipases and esteraseshttp://www.led.uni-stuttgart.de/
524LOX-DBMammalian, invertebrate, plant and fungal lipoxygenaseshttp://www.dkfz-heidelberg.de/spec/lox-db/
177MEROPSDatabase of proteolytic enzymes (peptidases)http://merops.sanger.ac.uk/
369NPDNuclear protein databasehttp://npd.hgu.mrc.ac.uk/
546NucleaRDBNuclear receptor superfamilyhttp://www.receptors.org/NR/
182Nuclear Receptor ResourceNuclear receptor superfamilyhttp://nrr.georgetown.edu/NRR/nrrhome.htm
183NUREBASENuclear hormone receptors databasehttp://www.ens-lyon.fr/LBMC/laudet/nurebase.html
184Olfactory Receptor DatabaseSequences for olfactory receptor-like moleculeshttp://senselab.med.yale.edu/senselab/ordb/
185ooTFDObject-oriented transcription factors databasehttp://www.ifti.org/ootfd
188PKRProtein kinase resource: sequences, enzymology, genetics and molecular and structural propertieshttp://pkr.sdsc.edu/html/index.shtml
759PLPMDBPyridoxal-5'-phosphate dependent enzymes mutationshttp://www.studiofmp.com/plpmdb/
609ProLysEDA database of bacterial protease systemshttp://genome.ukm.my/prolyses/
192ProlysisProteases and natural and synthetic protease inhibitorshttp://delphi.phys.univ-tours.fr/Prolysis/
224REBASERestriction enzymes and associated methylaseshttp://rebase.neb.com/rebase/rebase.html
195Ribonuclease P DatabaseRNase P sequences, alignments and structureshttp://www.mbio.ncsu.edu/RNaseP/home.html
573RPGRibosomal protein gene databasehttp://ribosome.miyazaki-med.ac.jp/
575RTKdbReceptor tyrosine kinase sequenceshttp://pbil.univ-lyon1.fr/RTKdb/
309S/MARt dBNuclear scaffold/matrix attached regionshttp://smartdb.bioinf.med.uni-goettingen.de/
741ScorpionDatabase of scorpion toxinshttp://research.i2r.a-star.edu.sg:8080/scorpion/
372SDAPStructural database of allergenic proteins and food allergenshttp://fermi.utmb.edu/SDAP
196SENTRASensory signal transduction proteinshttp://www-wit.mcs.anl.gov/sentra/
373SEVENS7-transmembrane helix receptors (G-protein-coupled)http://sevens.cbrc.jp/
248SRPDBProteins of the signal recognition particleshttp://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
314TrSDBTranscription factor databasehttp://ibb.uab.es/trsdb
399VKCDBVoltage-gated potassium channel databasehttp://vkcdb.biology.ualberta.ca/
202Wnt DatabaseWnt proteins and phenotypeshttp://www.stanford.edu/~rnusse/wntwindow.html
4. Structure Databases
4.1. Small molecules
646ChEBIChemical entities of biological interesthttp://www.ebi.ac.uk/chebi/
261CSDCambridge structural database: crystal structure information for organic and metal-organic compoundshttp://www.ccdc.cam.ac.uk/prods/csd/csd.html
265HIC-UpHetero-compound Information Centre—Uppsalahttp://xray.bmc.uu.se/hicup
402AANTAmino acid–nucleotide interaction databasehttp://aant.icmb.utexas.edu/
111KlothoCollection and categorization of biological compoundshttp://www.biocheminfo.org/klotho
113LIGANDChemical compounds and reactions in biological pathways
615PDB-Ligand3D structures of small molecules bound to proteins and nucleic acidshttp://www.idrtech.com/PDB-Ligand/
735PubChemStructures and biological activities of small organic moleculeshttp://pubchem.ncbi.nlm.nih.gov/
4.2. Carbohydrates
429CCSDComplex carbohydrate structure database (CarbBank)http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
652CSSCarbohydrate structure suite: carbohydrate 3D structures derived from the PDBhttp://www.dkfz.de/spec/css/
486GlycanCarbohydrate database, part of the KEGG system
292GlycoSuiteDBN- and O-linked glycan structures and biological sourceshttp://www.glycosuite.com/
535Monosaccharide BrowserSpace-filling Fischer projections of monosaccharideshttp://www.jonmaber.demon.co.uk/monosaccharide
300SWEET-DBAnnotated carbohydrate structure and substance informationhttp://www.dkfz-heidelberg.de/spec2/sweetdb/
4.3. Nucleic acid structure
272NDBNucleic acid-containing structureshttp://ndbserver.rutgers.edu/
273NTDBThermodynamic data for nucleic acidshttp://ntdb.chem.cuhk.edu.hk/
387RNABaseRNA-containing structures from PDB and NDBhttp://www.rnabase.org/
283SCORStructural classification oRNA: RNA motifs by structure, function and tertiary interactionshttp://scor.lbl.gov/
4.4. Protein structure
413ArchDBAutomated classification of protein loop structureshttp://gurion.imim.es/archdb
255ASTRALSequences of domains of known structure, selected subsets and sequence–structure correspondenceshttp://astral.stanford.edu/
288BAliBASEA database for comparison of multiple sequence alignmentshttp://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
257BioMagResBankNMR spectroscopic data for proteins and nucleic acidshttp://www.bmrb.wisc.edu/
384CADBConformational angles in proteins databasehttp://cluster.physics.iisc.ernet.in/cadb/
258CATHProtein domain structures databasehttp://www.biochem.ucl.ac.uk/bsm/cath_new
259CE3D protein structure alignmentshttp://cl.sdsc.edu/ce.html
260CKAAPs DBStructurally similar proteins with dissimilar sequenceshttp://ckaap.sdsc.edu/
442DaliProtein fold classification using the Dali search enginehttp://www.bioinfo.biocenter.helsinki.fi:8080/dali/
385Decoys ‘R’ UsComputer-generated protein conformationshttp://dd.stanford.edu/
447DisProtDatabase of Protein Disorder: proteins that lack fixed 3D structure in their native stateshttp://divac.ist.temple.edu/disprot
448DomInsDomain insertions in known protein structureshttp://stash.mrc-lmb.cam.ac.uk/DomIns
264DSDBASENative and modeled disulfide bonds in proteinshttp://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
386DSMMDatabase of simulated molecular motionshttp://projects.villa-bosch.de/dbase/dsmm/
452eF-siteElectrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active siteshttp://ef-site.protein.osaka-u.ac.jp/eF-site
674GenDiSGenomic distribution of protein structural superfamilieshttp://caps.ncbs.res.in/gendis/home.html
472Gene3DPrecalculated structural assignments for whole genomeshttp://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
489GTDGenomic threading database: structural annotations of complete proteomeshttp://bioinf.cs.ucl.ac.uk/GTD
322GTOPProtein fold predictions from genome sequenceshttp://spock.genes.nig.ac.jp/~genome/
360Het-PDB NaviHetero-atoms in protein structureshttp://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
498HOMSTRADHomologous structure alignment database: curated structure-based alignments for protein familieshttp://www-cryst.bioc.cam.ac.uk/homstrad
267IMB Jena Image LibraryVisualization and analysis of 3D biopolymer structureshttp://www.imb-jena.de/IMAGE.html
502IMGT/3Dstructure-DBSequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteinshttp://imgt3d.igh.cnrs.fr/
268ISSDIntegrated sequence–structure databasehttp://www.protein.bio.msu.su/issd
269LPFCLibrary of protein family core structureshttp://www-smi.stanford.edu/projects/helix/LPFC
270MMDBNCBI's database of 3D structures, part of NCBI Entrezhttp://www.ncbi.nlm.nih.gov/Structure
456E-MSDEBI's macromolecular structure databasehttp://www.ebi.ac.uk/msd
331ModBaseAnnotated comparative protein structure modelshttp://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
262MolMovDBDatabase of macromolecular movements: descriptions of protein and macromolecular motions, including movieshttp://bioinfo.mbb.yale.edu/MolMovDB/
274PALIPhylogeny and alignment of homologous protein structureshttp://pauling.mbu.iisc.ernet.in/~pali
275PASS2Structural motifs of protein superfamilieshttp://ncbs.res.in/~faculty/mini/campass/pass.html
557PepConfDBdatabase of peptide conformationshttp://www.peptidome.org/products/list.htm
276PDBProtein structure databank: all publicly available 3D structures of proteins and nucleic acidshttp://www.rcsb.org/pdb
277PDB-REPRDBRepresentative protein chains, based on PDB entrieshttp://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
278PDBsumSummaries and analyses of PDB structureshttp://www.biochem.ucl.ac.uk/bsm/pdbsum
619PDB_TMTransmembrane proteins with known 3D structurehttp://www.enzim.hu/PDB_TM/
719Protein Folding DatabaseExperimental data on protein foldinghttp://pfd.med.monash.edu.au/
282SCOPStructural classification oproteinshttp://scop.mrc-lmb.cam.ac.uk/scop
284SloopClassification of protein loopshttp://www-cryst.bioc.cam.ac.uk/~sloop/
583Structure Superposition DatabasePairwise superposition of TIM-barrel structureshttp://ssd.rbvi.ucsf.edu/
585SWISS-MODEL RepositoryDatabase of annotated 3D protein structure modelshttp://swissmodel.expasy.org/repository
285SUPERFAMILYAssignments of proteins to structural superfamilieshttp://supfam.org/
584SURFACESurface residues and functions annotated, compared and evaluated: a database of protein surface patcheshttp://cbm.bio.uniroma2.it/surface
764TargetDBTarget data from worldwide structural genomics projectshttp://targetdb.pdb.org/
4013D-GENOMICSStructural annotations for complete proteomeshttp://www.sbg.bio.ic.ac.uk/3dgenomics
310TOPSTopology oprotein structures databasehttp://www.tops.leeds.ac.uk/
5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature
73GenewHuman gene nomenclature: approved gene symbolshttp://www.gene.ucl.ac.uk/nomenclature
487GOGene ontology consortium databasehttp://www.geneontology.org/
389GOAEBI's gene ontology annotation projecthttp://www.ebi.ac.uk/GOA
513IUBMB Nomenclature databaseNomenclature of enzymes, membrane transporters, electron transport proteins and other proteinshttp://www.chem.qmul.ac.uk/iubmb
514IUPAC Nomenclature databaseNomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commissionhttp://www.chem.qmul.ac.uk/iupac
515IUPHAR-RDThe International Union of Pharmacology recommendations on receptor nomenclature and drug classificationhttp://www.iuphar-db.org/iuphar-rd/
552PANTHERGene products organized by biological functionhttp://panther.celera.com/
317UMLSUnified medical language systemhttp://umlsks.nlm.nih.gov/
5.1.1. Taxonomy and Identification
78ICBgyrB database for identification and classification of bacteriahttp://seasquirt.mbio.co.jp/icb/index.php
297NCBI TaxonomyNames of all organisms represented in GenBankhttp://www.ncbi.nlm.nih.gov/Taxonomy/
608PANDITProtein and associated nucleotide domains with inferred treeshttp://www.ebi.ac.uk/goldman-srv/pandit/
299RIDOMrRNA-based differentiation of medical microorganismshttp://www.ridom-rdna.de/
243RDP-IIRibosomal database projecthttp://rdp.cme.msu.edu/
301Tree of LifeInformation on phylogeny and biodiversityhttp://phylogeny.arizona.edu/tree/phylogeny.html
5.2. General genomics databases
7COGClusters of orthologous groups of proteinshttp://www.ncbi.nlm.nih.gov/COG
650COGENTComplete genome tracking: predicted peptides from fully sequenced genomeshttp://maine.ebi.ac.uk:8000/services/cogent/
337CORGComparative regulatory genomics: conserved non-coding sequence blockshttp://corg.molgen.mpg.de/
445DEGDatabase of essential genes from bacteria and yeasthttp://tubic.tju.edu.cn/deg
451EBI GenomesEBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomeshttp://www.ebi.ac.uk/genomes
453EGOEukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indiceshttp://www.tigr.org/tdb/tgi/ego/
70EMGlibEnhanced microbial genomes library: completely sequenced genomes of unicellular organismshttp://pbil.univ-lyon1.fr/emglib/emglib.html
458Entrez GenomesNCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomeshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
461ERGOLightIntegrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO databasehttp://www.ergo-light.com/ERGO
470FusionDBDatabase of bacterial and archaeal gene fusion eventshttp://igs-server.cnrs-mrs.fr/FusionDB
611Genome AtlasDNA structural properties of sequenced genomeshttp://www.cbs.dtu.dk/services/GenomeAtlas/
484Genome Information BrokerDDBJ's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomeshttp://gib.genes.nig.ac.jp/
678Genome ReviewsIntegrated view of complete genomeshttp://www.ebi.ac.uk/GenomeReviews/
75GOLDGenomes online database: a listing of completed and ongoing genome projectshttp://www.genomesonline.org/
352HGT-DBPutative horizontally transferred genes in prokaryotic genomeshttp://www.fut.es/~debb/HGT/
223Integr8Functional classification of proteins in whole genomeshttp://www.ebi.ac.uk/integr8/
112KEGGKyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathwayshttp://www.genome.jp/kegg
528MBGDMicrobial genome database for comparative analysis
549ORFanageDatabase of orphan ORFs (ORFs with no homologs) in complete microbial genomeshttp://www.cs.bgu.ac.il/~nomsiew/ORFans
551PACRATArchaeal and bacterial intergenic sequence featureshttp://www.biosci.ohio-tate.edu/~pacrat
715PartiGeneDBAssembled partial genomes for 250 eukaryotic organismshttp://www.partigenedb.org/
354PEDANTResults of an automated analysis of genomic sequenceshttp://pedant.gsf.de/
99TIGR Microbial DatabaseLists of completed and ongoing genome projects with links to complete genome sequenceshttp://www.tigr.org/tdb/mdb/mdbcomplete.html
66TIGR Comprehensive Microbial ResourceVarious data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteinshttp://www.tigr.org/CMR
311TransportDBPredicted membrane transporters in complete genomes, classified according to the TC classification systemhttp://www.membranetransport.org/
118WIT3What ithere? Metabolic reconstruction for completely sequenced microbial genomeshttp://www-wit.mcs.anl.gov/wit3/
5.3. Organism-specific databases
5.3.1. Viruses
473HCVDBThe hepatitis C virus databasehttp://hepatitis.ibcp.fr/
497HIV Drug Resistance DatabaseHIV mutations that confer resistance to anti-HIV drugshttp://resdb.lanl.gov/Resist_DB/default.htm
168HIV Molecular Immunology DatabaseHIV epitopeshttp://hiv-web.lanl.gov/immunology/
365HIV RT and Protease Sequence DatabaseHIV reverse transcriptase and protease sequenceshttp://hivdb.stanford.edu/
602NCBI Viral GenomesViral genome resource at NCBIhttp://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html
725Poxvirus.orgPoxvirus genomic sequences and gene annotationhttp://www.poxvirus.org/
750T4-like genome databaseSequences of T4-like bacteriophages from various sourceshttp://phage.bioc.tulane.edu/
201VIDAHomologous viral protein families databasehttp://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
761VIPERVirus particle explorer: virus capsid structureshttp://mmtsb.scripps.edu/viper
303VirOligoVirus-specific oligonucleotides for PCR and hybridizationhttp://viroligo.okstate.edu/
5.3.2. Prokaryotes
641BacMapPicture atlas of annotated bacterial genomeshttp://wishart.biology.ualberta.ca/BacMap
614MetaGrowthGrowth requirements of bacterial pathogenshttp://igs-server.cnrs-mrs.fr/axenic/
720PGTdbProkaryotic growth temperature databasehttp://pgtdb.csie.ncu.edu.tw/
5.3.2.1. Escherichia coli
415ASAPA systematic annotation package for community analysis of E.coli and related genomeshttps://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
428CyberCell databaseA collection of data on E.coli K12 intended for mathematical modeling to simulate the bacterial cellhttp://redpoll.pharmacy.ualberta.ca/CCDB
436coliBaseA database for E.coliSalmonella and Shigellahttp://colibase.bham.ac.uk/
437ColibriE.coli genome database at Institut Pasteurhttp://genolist.pasteur.fr/Colibri/
623EchoBASEPost-genomic studies of Escherichia colihttp://www.ecoli-york.org/
462Essential genes in E.coliFirst results of an E.coli gene deletion projecthttp://www.genome.wisc.edu/resources/essential.htm
482GenoBaseE.coli genome database at Nara Institutehttp://ecoli.aist-nara.ac.jp/
165GenProtECE.coli K12 genome and proteome databasehttp://genprotec.mbl.edu/
555PECProfiling of E.coli chromosomehttp://shigen.lab.nig.ac.jp/ecoli/pec
108EcoCycE.coli K12 genes, metabolic pathways, transporters and gene regulationhttp://ecocyc.org/
69EcoGeneSequence and literature data on E.coli genes and proteinshttp://bmb.med.miami.edu/EcoGene/EcoWeb/
116RegulonDBTranscriptional regulation and operon organization in E.colihttp://www.cifn.unam.mx/Computational_Genomics/regulondb/
5.3.2.2. Bacillus subtilis
424BSORFBacillus subtilis genome database at Kyoto U.
89NRSubNon-redundant Bacillus subtilis database at U. Lyonhttp://pbil.univ-lyon1.fr/nrsub/nrsub.html
96SubtiListBacillus subtilis genome database at Institut Pasteurhttp://genolist.pasteur.fr/SubtiList/
5.3.2.3. Other bacteria
420BioCycPathway/genome databases for many bacteriahttp://biocyc.org/
426CampyDBDatabase for Campylobacter genome analysishttp://campy.bham.ac.uk/
433ClostriDBFinished and unfinished genomes of Clostridium spp.http://clostri.bham.ac.uk/
648CIDBChlamydia Interactive Database: gene expression datahttp://www.it.deakin.edu.au/CIDB
68CyanoBaseCyanobacterial genomeshttp://www.kazusa.or.jp/cyano
521LeptoListLeptospira interrogans genomehttp://bioinfo.hku.hk/LeptoList
534MolliGenGenomic data on mollicuteshttp://cbi.labri.fr/outils/molligen/
733PseudoCAPPseudomonas aeruginosa genome database and community annotation projecthttp://www.pseudomonas.com/
94RsGDBRhodobacter sphaeroides genomehttp://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/
762VirFactBacterial virulence factors and pathogenicity islandshttp://virfact.burnham.org/
760Virulence FactorsReference database for microbial virulence factorshttp://zdsys.chgb.org.cn/VFs/main.htm
5.3.3. Unicellular eukaryotes
409ApiEST-DBEST sequences from various Apicomplexan parasiteshttp://www.cbil.upenn.edu/paradbs-servlet
439CryptoDBCryptosporidium parvum genome databasehttp://cryptodb.org/
662Diatom EST DatabaseESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutumhttp://avesthagen.sznbowler.com/
446DictyBaseUniversal resource for Dictyostelium discoideumhttp://dictybase.org/
72Full-MalariaFull-length cDNA library from erythrocytic-stage Plasmodium falciparumhttp://fullmal.ims.u-tokyo.ac.jp/
328GeneDBCurated database for various Sanger-sequenced genomeshttp://www.genedb.org/
698LumbriBASEESTs of the earthworm Lumbricus rubellushttp://www.earthworms.org/
91PlasmoDBPlasmodium genome databasehttp://plasmodb.org/
586TcruziDBTrypanosoma cruzi genome databasehttp://tcruzidb.org/
359ToxoDBToxoplasma gondii genome databasehttp://toxodb.org/
5.3.4. Fungi
5.3.4.1. Yeasts
635AGDAshbya gossypii genome databasehttp://agd.unibas.ch/
617CandidaDBCandida albicans genome databasehttp://genolist.pasteur.fr/CandidaDB
645Candida GenomeCandida albicans genome databasehttp://www.candidagenome.org/
441CYGDMIPS Comprehensive yeast genome databasehttp://mips.gsf.de/proj/yeast
483GénolevuresA comparison of S.cerevisiae and 14 other yeast specieshttp://cbi.labri.fr/Genolevures
730PROPHECYProfiling of phenotypic characteristics in yeasthttp://prophecy.lundberg.gu.se/
576SCMDSaccharomyces cerevisiae morphological database: micrographs of budding yeast mutantshttp://yeast.gi.k.u-tokyo.ac.jp/
577SCPDSaccharomyces cerevisiae promoter databasehttp://cgsigma.cshl.org/jian
357SGDSaccharomyces genome databasehttp://www.yeastgenome.org/
25TRIPLESTransposon-insertion phenotypes, localization and expression in Saccharomyceshttp://ygac.med.yale.edu/triples/
306YDPMYeast deletion project and mitochondria databasehttp://www-deletion.stanford.edu/YDPM/YDPM_index.html
342Yeast Intron DatabaseAres lab database of splicesomal introns in S.cerevisiaehttp://www.cse.ucsc.edu/research/compbio/yeast_introns.html
254Yeast snoRNA DatabaseYeast small nucleolar RNAshttp://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
307yMGVYeast microarray global viewerhttp://www.transcriptome.ens.fr/ymgv/
763YRC PDRYeast resource center public data repositoryhttp://www.yeastrc.org/pdr/
5.3.4.2. Other fungi
425CADRECentral Aspergillus data repositoryhttp://www.cadre.man.ac.uk/
435COGEMEPhytopathogenic fungi and oomycete EST databasehttp://cogeme.ex.ac.uk/
533MNCDBMIPS Neurospora crassa databasehttp://mips.gsf.de/proj/neurospora/
708OGDOomycete Genomics Database: ESTs and annotationhttp://www.oomycete.net/
98Phytophthora Functional Genomics DatabaseESTs and expression data from P.infestans and P.sojaehttp://www.pfgd.org/pfgd/
5.3.5. Invertebrates
5.3.5.1. Caenorhabditis elegans
430C.elegans ProjectGenome sequencing data at the Sanger Institutehttp://www.sanger.ac.uk/Projects/C_elegans
238IntroneratorIntrons and splicing in C.elegans and C.briggsaehttp://www.cse.ucsc.edu/~kent/intronerator/
570RNAiDBRNAi phenotypic analysis of C.elegans geneshttp://www.rnai.org/
100WILMAC.elegans annotation databasehttp://www.came.sbg.ac.at/wilma/
304WorfDBC.elegans ORFeomehttp://worfdb.dfci.harvard.edu/
51WormBaseData repository for C.elegans and C.briggsae: curated genome annotation, genetic and physical maps, pathwayshttp://www.wormbase.org/
5.3.5.2. Drosophila melanogaster
71FlyBaseDrosophila sequences and genomic informationhttp://flybase.bio.indiana.edu/
767FlyBrainDatabase of the Drosophila nervous systemhttp://flybrain.neurobio.arizona.edu/
670FlyMineIntegration of insect genomic and proteomic datahttp://www.flymine.org/
467FlyTrapDrosophila mutants created using GFP protein trap strategyhttp://flytrap.med.yale.edu/
471GadFlyGenome annotation database of Drosophilahttp://www.fruitfly.org/
677GeniSysEnhancer- and promoter-inserted mutants of Drosophilahttp://genisys.kaist.ac.kr:8080/
774DPDBDrosophila polymorphism databasehttp://dpdb.uab.es/
449Drosophila microarray projectData and tools for Drosophila gene expression studieshttp://www.flyarrays.com/fruitfly
509InterActive FlyDrosophila genes and their roles in developmenthttp://sdb.bio.purdue.edu/fly/aimain/1aahome.htm
5.3.5.3. Other invertebrates
410AppaDBA database on the nematode Pristionchus pacificushttp://appadb.eb.tuebingen.mpg.de/
643BeetleBaseGenome database of the beetle Tribolium castaneumhttp://www.bioinformatics.ksu.edu/BeetleBase/
649Ciliate IES-MDS DbMacro- and micronuclear genes in spirotrichous ciliateshttp://oxytricha.princeton.edu/dimorphism/database.htm
434CnidBaseCnidarian evolution and gene expression databasehttp://cnidbase.bu.edu/
543Nematode.netParasitic nematode sequencing projecthttp://nematode.net/
544NEMBASENematode sequence and functional data databasehttp://www.nematodes.org/
726PPNEMAPlant-parasitic nematode rRNAshttp://bighost.area.ba.cnr.it/PPNEMA/
743SilkDBSilkworm Bombyx mori ESTs, mutants, photographshttp://www.ab.a.u-tokyo.ac.jp/genome/
744SilkSatDbA microsatellite database of the silkworm Bombyx morihttp://www.cdfd.org.in/silksatdb/
747SpodoBaseGenomics of the butterfly Spodoptera frugiperdahttp://bioweb.ensam.inra.fr/spodobase/
6. Metabolic Enzymes and Pathways; Signaling Pathways
6.1. Enzymes and Enzyme Nomenclature
421BRENDAEnzyme names and biochemical propertieshttp://www.brenda.uni-koeln.de/
109ENZYMEEnzyme nomenclature and propertieshttp://www.expasy.org/enzyme
459Enzyme NomenclatureIUBMB Nomenclature Committee recommendationshttp://www.chem.qmw.ac.uk/iubmb/enzyme
613EzCatDBEnzyme Catalytic Mechanism Databasehttp://mbs.cbrc.jp/EzCatDB/
508IntEnzIntegrated enzyme database and enzyme nomenclaturehttp://www.ebi.ac.uk/intenz
716PDBrtfRepresentation of target families of enzymes in PDBhttp://cgl.imim.es/pdbrtf/
758SCOPECMapping of catalytic function to domain structurehttp://www.enzome.com/databases/scopec.php
6.2. Metabolic Pathways
644BioSilicoIntegrated access to various metabolic databaseshttp://biosilico.kaist.ac.kr/
112KEGG PathwayMetabolic and regulatory pathways in complete genomeshttp://www.genome.jp/kegg/pathway.html
114MetaCycMetabolic pathways and enzymes from various organismshttp://metacyc.org/
115PathDBBiochemical pathways, compounds and metabolismhttp://www.ncgr.org/pathdb
117UM-BBDUniversity of Minnesota biocatalysis and biodegradation databasehttp://umbbd.ahc.umn.edu/
6.3. Intermolecular Interactions and Signaling Pathways
6333DID3D interacting domains: domain–domain interactions in proteins with known 3D structureshttp://3did.embl.de/
405aMAZEA system for the annotation, management, and analysis of biochemical and signalling pathway networkshttp://www.amaze.ulb.ac.be/
103BINDBiomolecular interaction network databasehttp://www.bind.ca/
419BioCartaOnline maps of metabolic and signaling pathwayshttp://www.biocarta.com/genes/allPathways.asp
422BRITEBiomolecular relations in information transmission and expression, part of KEGG
659DDIBDatabase of domain interactions and bindinghttp://www.ddib.org/
104DIPDatabase of interacting proteins: experimentally determined protein–protein interactionshttp://dip.doe-mbi.ucla.edu/
105DRCDatabase of ribosomal crosslinkshttp://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc
329GeneNetDatabase on gene network componentshttp://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet
664hp-DPIDatabase of protein interactions in Helicobacter pylorihttp://dpi.nhri.org.tw/hp/
688HPIDHuman protein interaction databasehttp://www.hpid.org/
507IntAct projectProtein–protein interaction datahttp://www.ebi.ac.uk/intact
770Inter-Chain Beta-SheetsProtein–protein interactions mediated by interchain beta-sheet formationhttp://www.igb.uci.edu/servers/icbs/
510InterDomPutative protein domain interactionshttp://interdom.lit.org.sg/
718PDZBaseProtein–protein interactions involving PDZ domainshttp://icb.med.cornell.edu/services/pdz/start
749Protein-protein interfacesInteracting residues in protein–protein interfaces in PDBhttp://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
773PINdbProteins interacting in nucleus (human and yeast)http://pin.mskcc.org/
748POINTPrediction of human protein–protein interactomehttp://point.nchc.org.tw/
616PSIbaseInteraction of proteins with known 3D structureshttp://psimap.kaist.ac.kr/
612ReactomeA knowledgebase of biological pathwayshttp://www.reactome.org/
571ROSPathReactive oxygen species (ROS) signaling pathwayhttp://rospath.ewha.ac.kr/
395STCDBSignal transductions classification databasehttp://bibiserv.techfak.uni-bielefeld.de/stcdb/
582STRINGPredicted functional associations between proteinshttp://string.embl.de/
341TRANSPATHGene regulatory networks and microarray analysishttp://www.biobase.de/pages/products/databases.html
7. Human and other Vertebrate Genomes
7.1. Model organisms, comparative genomics
63ACeDBC.elegansS.pombe and human genomic informationhttp://www.acedb.org/
26AllGenesHuman and mouse gene, transcript and protein annotationhttp://www.allgenes.org/
65ArkDBGenome databases for farm and other animalshttp://www.thearkdb.org/
647ChickVDSequence variation in the chicken genomehttp://chicken.genomics.org.cn/
286Cre Transgenic DatabaseCre transgenic mouse lines with links to publicationshttp://www.mshri.on.ca/nagy/
660DEDDatabase of evolutionary distanceshttp://warta.bio.psu.edu/DED/
27EnsemblAnnotated information on eukaryotic genomeshttp://www.ensembl.org/
465FANTOMFunctional annotation omouse full-length cDNA cloneshttp://fantom2.gsc.riken.go.jp/
468FREPFunctional repeats in mouse cDNAshttp://facts.gsc.riken.go.jp/FREP/
673GALAGenomic alignment, annotation and experimental resultshttp://gala.cse.psu.edu/
347GenetPigGenes controlling economic traits in pighttp://www.infobiogen.fr/services/Genetpig
605HomoloGeneAutomatically detected homologous genes in complete eukaryotic genomeshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
690InparanoidA database of eukaryotic orthologshttp://inparanoid.cgb.ki.se/
696IPIInternational protein index: non-redundant sets of human, mouse and rat proteinshttp://www.ebi.ac.uk/IPI
777KaryotypeDBKaryotype and chromosome information for animal and plant specieshttp://www.nenno.it/karyotypedb/
400KOGEukaryotic orthologous groups of proteinshttp://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi
87Mouse Genome InformaticsFormerly mouse genome databasehttp://www.informatics.jax.org/
540MTIDMouse transposon insertion databasehttp://mouse.ccgb.umn.edu/transposon/
703NegProtNegative Proteome: a tool for comparison of complete proteomeshttp://superfly.ucsd.edu/negprot
556PEDEPig EST data explorer: full-length cDNAs and ESTshttp://pede.gene.staff.or.jp/
665PhenomicDBComparison of phenotypes of orthologous genes in human and model organismshttp://www.phenomicdb.de/
724PolymorphixA database of sequence polymorphismshttp://pbil.univ-lyon1.fr/polymorphix/query.php
93Rat Genome DatabaseRat genetic and genomic datahttp://rgd.mcw.edu/
625RatMapRat genome tools and datahttp://ratmap.org/
751TAEDThe adaptive evolution database: a phylogeny-based tool for comparative genomicshttp://www.bioinfo.no/tools/TAED
5TIGR Gene IndicesOrganism-specific databases of EST and gene sequenceshttp://www.tigr.org/tdb/tgi.shtml
6UniGeneUnified clusters of ESTs and full-length mRNA sequenceshttp://www.ncbi.nlm.nih.gov/UniGene/
319UniSTSUnified view of sequence tagged sites with mapping datahttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
783VEGAVertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequenceshttp://vega.sanger.ac.uk/
101ZFINZebrafish information networkhttp://zfin.org/
7.2. Human genome databases, maps and viewers
27EnsemblAnnotated information on eukaryotic genomeshttp://www.ensembl.org/
404AluGeneComplete Alu map in the human genomehttp://alugene.tau.ac.il/
349CroW 21Human chromosome 21 databasehttp://bioinfo.weizmann.ac.il/crow21/
55GB4-RHGenebridge4 human radiation hybrid mapshttp://www.sanger.ac.uk/Software/RHserver/RHserver.shtml
56GDBHuman genes and genomic mapshttp://www.gdb.org/
57GenAtlasHuman genes, markers and phenotypeshttp://www.genatlas.org/
350GeneCardsIntegrated database of human genes, maps, proteins and diseaseshttp://bioinfo.weizmann.ac.il/cards/
348GeneLocGene location database (formerly UDB—Unified database for human genome mapping)http://genecards.weizmann.ac.il/geneloc/
327GeneNestGene indices of human, mouse, zebrafish, etc.http://genenest.molgen.mpg.de/
59GenMapDBMapped human BAC cloneshttp://genomics.med.upenn.edu/genmapdb
35Gene Resource LocatorAlignment of ESTs with finished human sequencehttp://grl.gi.k.u-tokyo.ac.jp/
324HOWDYHuman organized whole genome databasehttp://www-alis.tokyo.jst.go.jp/HOWDY/
60HuGeMapHuman genome genetic and physical map datahttp://www.infobiogen.fr/services/Hugemap
77Human BAC EndsNon-redundant human BAC end sequenceshttp://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
597Human Genome Segmental Duplication DatabaseSegmental duplications in the human genomehttp://projects.tcag.ca/humandup
61IXDBPhysical maps of human chromosome Xhttp://ixdb.mpimg-berlin-dahlem.mpg.de/
697L1BaseFunctional annotation and prediction of LINE-1 elementshttp://line1.molgen.mpg.de/
54Map ViewerDisplay of genomic information by chromosomal positionhttp://www.ncbi.nlm.nih.gov/mapview/
600MGCMammalian genome collection: full-length ORFs for human, mouse and rat geneshttp://mgc.nci.nih.gov/
391NCBI RefSeqNon-redundant collection of naturally occurring biological moleculeshttp://www.ncbi.nlm.nih.gov/RefSeq/
553ParaDBParalogy mapping in human genomeshttp://abi.marseille.inserm.fr/paradb/
62RHdbRadiation hybrid map datahttp://www.ebi.ac.uk/RHdb
592SKY/M-FISH and CGHFluorescent images of chromosomes and cytogenetic datahttp://www.ncbi.nlm.nih.gov/sky/
4STACKSequence tag alignment and consensus knowledgebasehttp://www.sanbi.ac.za/Dbases.html
596The Chromosome 7 Annotation ProjectA comprehensive description of human chromosome 7http://www.chr7.org/
684TRBaseTandem repeats in the human genomehttp://bioinfo.ex.ac.uk/trbase
316UCSC Genome BrowserGenome assemblies and annotationhttp://genome.ucsc.edu/
7.3. Human proteins
685H-InvDBFull-length human cDNA cloneshttp://www.h-invitational.jp/
499HPMRHuman plasma membrane receptome: sequences, literature and expression datahttp://receptome.stanford.edu/
500HPRDHuman protein reference database: domain architecture, post-translational modifications and disease associationhttp://www.hprd.org/
37HUNTHuman novel transcripts: annotated full-length cDNAshttp://www.hri.co.jp/HUNT
171HUGEHuman unidentified gene-encoded large (>50 kDa) protein and cDNA sequenceshttp://www.kazusa.or.jp/huge
522LIFEdbLocalization, interaction and functions of human proteinshttp://www.dkfz.de/LIFEdb
312trome, trEST and trGEN:Databases of predicted human protein sequencesftp://ftp.isrec.isb-sib.ch/pub/databases/
8. Human Genes and Diseases
8.1. General Databases
661DG-CSTDisease gene conserved sequence tagshttp://143.225.208.11/cst3/
683HCADHuman chromosome aberration database: chromosomal breakpoints and affected geneshttp://www.pdg.cnb.uam.es/UniPub/HCAD/
8HomophilaDrosophila homologs of human disease genes tohttp://superfly.ucsd.edu/homophila/
548OMIAOnline Mendelian inheritance in animals: a catalog of animal genetic and genomic disordershttp://www.angis.org.au/omia
143OMIMOnline Mendelian inheritance in man: a catalog of human genetic and genomic disordershttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
550ORFDBCollection of ORFs that are sold by Invitrogenhttp://orf.invitrogen.com/
554PathBaseEuropean mutant mice histopathology database: imageshttp://www.pathbase.net/
146PMDCompilation of protein mutant datahttp://pmd.ddbj.nig.ac.jp/
358SOURCEFunctional genomics resource for human, mouse and rathttp://source.stanford.edu/
8.2. Human Mutations Databases
8.2.1. General polymorphism databases
119ALFREDAllele frequencies and DNA polymorphismshttp://alfred.med.yale.edu/
416BayGenomicsGenes relevant to cardiovascular and pulmonary diseasehttp://baygenomics.ucsf.edu/
654Cypriot national mutation databaseDisease mutations in the Cypriot populationhttp://www.goldenhelix.org/cypriot/
655Database of Genomic VariantsHuman genomic variants: frequency, segmental duplications and genome assembly gapshttp://projects.tcag.ca/variation/
595dbQSNPQuantification of SNP allele frequencies databasehttp://qsnp.gen.kyushu-u.ac.jp/
127dbSNPDatabase of single nucleotide polymorphismshttp://www.ncbi.nlm.nih.gov/SNP/
669FESDFunctional element SNPs database: SNPs located within promoters, UTRs, etc., of human geneshttp://combio.kribb.re.kr/ksnp/resd/
496HGVS DatabasesA compilation of human mutation databaseshttp://www.hgvs.org/
131HGVbaseHuman genome variation database: curated human polymorphismshttp://hgvbase.cgb.ki.se/
133HGMDHuman gene mutation databasehttp://www.hgmd.org/
367IPDImmuno polymorphism databasehttp://www.ebi.ac.uk/ipd
517JSNPJapanese SNP databasehttp://snp.ims.u-tokyo.ac.jp/
45rSNP GuideSNPs in regulatory gene regionshttp://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
344SNP Consortium databaseSNP Consortium datahttp://snp.cshl.org/
626SNPeffectPhenotypic effects of human coding SNPshttp://snpeffect.vib.be/
590TopoSNPTopographic database of non-synonymous SNPshttp://gila.bioengr.uic.edu/snp/toposnp
755TPMDTaiwan polymorphic microsatellite marker databasehttp://tpmd.nhri.org.tw/
8.2.2. Cancer
122Atlas of Genetics and Cytogenetics in Oncology and HaematologyCancer-related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseaseshttp://www.infobiogen.fr/services/chromcancer/
593Cancer ChromosomesCytogenetic, clinical and reference information on cancer-related aberrationshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes
431CGEDCancer gene expression databasehttp://love2.aist-nara.ac.jp/CGED
651COSMICCatalogue osomatic mutations icancer: sequence data, samples and publicationshttp://www.sanger.ac.uk/perl/CGP/cosmic
126Germline p53 MutationsMutations in human tumor and cell line p53 genehttp://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm
362IARC TP53 DatabaseHuman TP53 somatic and germline mutationshttp://www.iarc.fr/p53/
152MTBMouse tumor biology database: tumor types, genes, classification, incidence, pathologyhttp://tumor.informatics.jax.org/
709OncoMineCancer microarray data by gene or cancer typehttp://www.oncomine.org/
153Oral Cancer Gene DatabaseCellular and molecular data for genes involved in oral cancerhttp://www.tumor-gene.org/Oral/oral.html
148RB1 Gene Mutation DBMutations in the human retinoblastoma (RB1) genehttp://www.d-lohmann.de/Rb/
574RTCGDMouse retroviral tagged cancer gene databasehttp://rtcgd.ncifcrf.gov/
579SNP500CancerRe-sequenced SNPs from 102 reference sampleshttp://snp500cancer.nci.nih.gov/
149SV40 Large T-Antigen MutantsMutations in SV40 large tumor antigen genehttp://supernova.bio.pitt.edu/pipaslab/
155Tumor Gene Family DatabasesCellular, molecular and biological data about genes involved in various cancershttp://www.tumor-gene.org/tgdf.html
8.2.3. Gene-, system- or disease-specific
768ALPSbaseAutoimmune lymphoproliferative syndrome databasehttp://research.nhgri.nih.gov/alps/
120Androgen Receptor Gene Mutations DatabaseMutations in the androgen receptor genehttp://www.mcgill.ca/androgendb/
123BTKbaseMutation registry for X-linked agammaglobulinemiahttp://bioinf.uta.fi/BTKbase/
594CarpeDBComprehensive database on the genetics of epilepsyhttp://www.carpedb.ua.edu/
124CASRDBCalcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidismhttp://www.casrdb.mcgill.ca/
125Cytokine Gene Polymorphism in Human DiseaseCytokine gene polymorphism literature databasehttp://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm
137Collagen Mutation DatabaseHuman type I and type III collagen gene mutationshttp://www.le.ac.uk/genetics/collagen/
460ERGDBEstrogen responsive genes databasehttp://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/
164FUNPEPLow-complexity peptides capable of forming amyloid plaquehttp://www.cmbi.kun.nl/swift/FUNPEP/gergo/
363GOLD.dbGenomics olipid-associated disorders databasehttp://gold.tugraz.at/
129GRAPMutants of G-protein coupled receptors of family Ahttp://tinygrap.uit.no/GRAP/
130HaemBFactor IX gene mutations, insertions and deletionshttp://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html
491HbVarHuman hemoglobin variants and thalassemiashttp://globin.cse.psu.edu/globin/hbvar
680HAGRHuman ageing genomic resources: genes related to ageing in humans and model organismshttp://genomics.senescence.info/
134Human p53/hprt, rodent lacI/lacZ databasesMutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutationshttp://www.ibiblio.org/dnam/mainpage.html
135Human PAX2 Allelic Variant DatabaseMutations in human PAX2 genehttp://pax2.hgu.mrc.ac.uk/
136Human PAX6 Allelic Variant DatabaseMutations in human PAX6 genehttp://pax6.hgu.mrc.ac.uk/
506INFEVERSHereditary inflammatory disorder and familial mediterranean fever mutation datahttp://fmf.igh.cnrs.fr/infevers
139KinMutBaseDisease-causing protein kinase mutationshttp://www.uta.fi/imt/bioinfo/KinMutBase/
523Lowe Syndrome Mutation DatabaseMutations causing Lowe oculocerebrorenal syndromehttp://research.nhgri.nih.gov/lowe/
142NCL Mutation DatabasePolymorphisms in neuronal ceroid lipofuscinoses geneshttp://www.ucl.ac.uk/ncl/
144PAHdbMutations at the phenylalanine hydroxylase locushttp://www.mcgill.ca/pahdb/
559PGDBProstate and prostatic diseases gene databasehttp://www.ucsf.edu/pgdb/
145PHEXdbPHEX mutations causing X-linked hypophosphatemiahttp://www.phexdb.mcgill.ca/
147PTCH1 Mutation DatabaseMutations and SNPs found in PTCH1 genehttp://www.cybergene.se/PTCH/ptchbase.html
SCAdbSpinocerebellar ataxia candidate gene databasehttp://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map
632T1DbaseA resource for type 1 diabetes researchhttp://t1dbase.org/
752The Autism Chromosome Rearrangement DatabaseCurated collection of genomic features related to autismhttp://projects.tcag.ca/autism
753The Lafora DatabaseMutations and polymorphisms associated with Lafora progressive myoclonus epilepsyhttp://projects.tcag.ca/lafora/
9. Microarray Data and other Gene Expression Databases
6345'SAGE5'-end serial analysis of gene expressionhttp://5sage.gi.k.u-tokyo.ac.jp/
338ArrayExpressPublic collection of microarray gene expression datahttp://www.ebi.ac.uk/arrayexpress
11AxeldbGene expression in Xenopus laevishttp://www.dkfz-heidelberg.de/abt0135/axeldb.htm
12BodyMapHuman and mouse gene expression datahttp://bodymap.ims.u-tokyo.ac.jp/
417BGEDBrain gene expression databasehttp://love2.aist-nara.ac.jp/BGED
432CleanExExpression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisonshttp://www.cleanex.isb-sib.ch/
657dbERGEIIDatabase of experimental results on gene expression: genomic alignment, annotation and experimental datahttp://dberge.cse.psu.edu/menu.html
454EICO DBExpression-based imprint candidate organiser: a database for discovery of novel imprinted geneshttp://fantom2.gsc.riken.jp/EICODB/
455emap AtlasEdinburgh mouse atlas: a digital atlas of mouse embryo development and spatially mapped gene expressionhttp://genex.hgu.mrc.ac.uk/
13EPConDBEndocrine pancreas consortium databasehttp://www.cbil.upenn.edu/EPConDB
110EpoDBGenes expressed during human erythropoiesishttp://www.cbil.upenn.edu/EpoDB/
14FlyViewDrosophila development and geneticshttp://pbio07.uni-muenster.de/
326GeneAnnotRevised annotation of Affymetrix human gene probe setshttp://genecards.weizmann.ac.il/geneannot/
325GeneNoteHuman genes expression profiles in healthy tissueshttp://genecards.weizmann.ac.il/genenote/
330GenePaintGene expression patterns in the mousehttp://www.genepaint.org/Frameset.html
676GeneTideA transcriptome-focused member of the GeneCards suitehttp://genecards.weizmann.ac.il/genetide/
481GeneTrapExpression patterns in an embryonic stem library of gene trap insertionshttp://www.cmhd.ca/sub/genetrap.asp
603GEOGene expression omnibus: gene expression profileshttp://www.ncbi.nlm.nih.gov/geo/
485GermOnlineGene expression in mitotic and meiotic cell cyclehttp://www.germonline.org/
15GXDMouse gene expression databasehttp://www.informatics.jax.org/menus/expression_menu.shtml
681H-ANGELHuman anatomic gene expression libraryhttp://www.jbirc.aist.go.jp/hinv/index.jsp
493HemBaseGenes expressed in differentiating human erythroid cellshttp://hembase.niddk.nih.gov/
23HugeIndexExpression levels of human genes in normal tissueshttp://hugeindex.org/
17Kidney Development DatabaseKidney development and gene expressionhttp://golgi.ana.ed.ac.uk/kidhome.html
778LOLAList olists annotated: a comparison of gene sets identified in different microarray experimentshttp://www.lola.gwu.edu/
18MAGESTAscidian (Halocynthia roretzi) gene expression patterns
699MAMEPMolecular anatomy of the mouse embryo project: gene expression data on mouse embryoshttp://mamep.molgen.mpg.de/
339MEPDMedaka (freshwater fish Oryzias latipes) gene expression pattern databasehttp://www.embl.de/mepd/
19MethDBDNA methylation data, patterns and profileshttp://www.methdb.de/
537Mouse SAGESAGE libraries from various mouse tissues and cell lineshttp://mouse.biomed.cas.cz/sage
541NASCarraysNottingham Arabidopsis Stock Centre microarray databasehttp://affymetrix.arabidopsis.info/
545NetAffxPublic Affymetrix probesets and annotationshttp://www.affymetrix.com/
711Osteo-Promoter DatabaseGenes in osteogenic proliferation and differentiationhttp://www.opd.tau.ac.il/
154PEDBProstate expression database: ESTs from prostate tissue and cell type-specific cDNA librarieshttp://www.pedb.org/
558PEPRPublic expression profiling resource: expression profiles in a variety of diseases and conditionshttp://microarray.cnmcresearch.org/pgadatatable.asp
21RECODEGenes using programmed translational recoding in their expressionhttp://recode.genetics.utah.edu/
568RefExAReference database for human gene expression analysishttp://www.lsbm.org/db/index_e.html
739rOGEDRat ovarian gene expression databasehttp://web5.mccs.uky.edu/kolab/rogedendo.aspx
712SAGEmapNCBI's resource for SAGE data from various organismshttp://www.ncbi.nlm.nih.gov/SAGE
742SIEGESmoking Induced Epithelial Gene Expressionhttp://pulm.bumc.bu.edu/siegeDB
22Stanford Microarray DatabaseRaw and normalized data from microarray experimentshttp://genome-www.stanford.edu/microarray
24Tooth Development DatabaseGene expression in dental tissuehttp://bite-it.helsinki.fi/
10. Proteomics Resources
6062D-PAGEProteome database system for microbial researchhttp://www.mpiib-berlin.mpg.de/2D-PAGE
731DynaProt 2DProteome database of Lactococcus lactishttp://www.wzw.tum.de/proteomik/lactis/
222GelBank2D gel electrophoresis patterns of proteins from complete microbial genomeshttp://gelbank.anl.gov/
710Open Proteomics DatabaseMass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacteriumhttp://bioinformatics.icmb.utexas.edu/OPD/
377PEPPredictions for entire proteomes: summarized analyses of protein sequenceshttp://cubic.bioc.columbia.edu/pep/
281RESIDPre-, co- and post-translational protein modificationshttp://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html
225SWISS-2DPAGEAnnotated 2D gel electrophoresis databasehttp://www.expasy.org/ch2d/
11. Other Molecular Biology Databases
11.1. Drugs and drug design
407ANTIMICDatabase of natural antimicrobial peptideshttp://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/
781AOBaseAntisense oligonucleotide selection and designhttp://www.bio-inf.net/aobase/
408APDAntimicrobial peptide databasehttp://aps.unmc.edu/AP/main.php
423BSDBiodegradative strain database: microorganisms that can degrade aromatic and other organic compoundshttp://bsd.cme.msu.edu/
443DARTDrug adverse reaction target databasehttp://xin.cz3.nus.edu.sg/group/drt/dart.asp
701MetaRouterCompounds and pathways related to bioremediationhttp://pdg.cnb.uam.es/MetaRouter/
186PeptaibolPeptaibol (antibiotic peptide) sequenceshttp://www.cryst.bbk.ac.uk/peptaibol/welcome.html
392PharmGKBPharmacogenomics knowledge base: effect of genetic variation on drug responseshttp://www.pharmgkb.org/
315TTDTherapeutic target databasehttp://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp
11.2. Probes
505IMGT/PRIMER-DBImmunogenetics oligonucleotide primer databasehttp://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl
296MPDBSynthetic oligonucleotides useful as primers or probeshttp://www.biotech.ist.unige.it/interlab/mpdb.html
728PrimerPCRPCR primers for eukaryotic and prokaryotic geneshttp://bioinfo.ebc.ee/PrimerStudio/
390probeBaserRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated informationhttp://www.microbial-ecology.net/probebase
736QPPDQuantitative PCR Primer Database for human and mousehttp://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp
356RTPrimerDBReal-time PCR primer and probe sequenceshttp://medgen.ugent.be/rtprimerdb/
11.3. Unclassified databases
298PubMedCitations and abstracts of biomedical literaturehttp://pubmed.gov/
256BioImageDatabase of multidimensional biological imageshttp://www.bioimage.org/
12. Organelle Databases
74GOBASEOrganelle genome databasehttp://megasun.bch.umontreal.ca/gobase/
547OGReOrganelle genome retrieval systemhttp://ogre.mcmaster.ca/
601Organelle genomesNCBI's organelle genome resourcehttp://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
722PLprotArabidopsis thaliana chloroplast protein databasehttp://www.pb.ipw.biol.ethz.ch/proteomics
713Organelle DBOrganelle proteins and subcellular structureshttp://organelledb.lsi.umich.edu/
12.1. Mitochondrial Genes and Proteins
637AMPDBArabidopsis mitochondrial protein databasehttp://www.mitoz.bcs.uwa.edu.au/AMPDB/
686HMPDHuman mitochondrial protein databasehttp://bioinfo.nist.gov:8080/examples/servlets/index.html
38HvrBasePrimate mitochondrial DNA control region sequenceshttp://www.hvrbase.org/
64MitochondriomeMetazoan mitochondrial geneshttp://www.ba.itb.cnr.it/mitochondriome
83MitoDatMitochondrial proteins (predominantly human)http://www-lecb.ncifcrf.gov/mitoDat/
226MitoDromeNuclear-encoded mitochondrial proteins of Drosophilahttp://www2.ba.itb.cnr.it/MitoDrome/
84MitoMapHuman mitochondrial genomehttp://www.mitomap.org/
85MitoNucNuclear genes coding for mitochondrial proteinshttp://www2.ba.itb.cnr.it/MitoNuc/
86MITOP2Mitochondrial proteins, genes and diseaseshttp://ihg.gsf.de/mitop2/start.jsp
531MitoPDYeast mitochondrial protein databasehttp://bmerc-www.bu.edu/mito
532MitoProteomeExperimentally described human mitochondrial proteinshttp://www.mitoproteome.org/
538MPIMPMitochondrial protein import machinery of plantshttp://millar3.biochem.uwa.edu.au/~lister/index.html
241PLMItRNAPlant mitochondrial tRNAhttp://bighost.area.ba.cnr.it/PLMItRNA/
13. Plant Databases
13.1. General plant databases
599BarleyBaseExpression profiling of plant genomeshttp://www.barleybase.org/
624CR-ESTCrop ESTs: barley, pea, wheat and potatohttp://pgrc.ipk-gatersleben.de/cr-est/
67CropNetGenome mapping in crop plantshttp://ukcrop.net/
128FLAGdb++Integrative database about plant genomeshttp://genoplante-info.infobiogen.fr/FLAGdb/
351GénoPlante-InfoPlant genomic data from the Génoplante consortiumhttp://genoplante-info.infobiogen.fr/
488GrainGenesGenes and phenotypes of wheat, barley, rye, triticale, oatshttp://wheat.pw.usda.gov/ or http://www.graingenes.org/
607GrameneA resource for comparative grass genomicshttp://www.gramene.org/
81MendelAnnotated plant ESTs and STSshttp://www.mendel.ac.uk/
581openSputnikPlant EST clustering and functional annotationhttp://sputnik.btk.fi/
560PhytoProtClusters of (predicted) plant proteinshttp://genoplante-info.infobiogen.fr/phytoprot
721PlantMarkersA database of predicted molecular markers from plantshttp://markers.btk.fi/
355PlantGDBPlant genome database: actively transcribed plant geneshttp://www.plantgdb.org/
189PLANT-PIsPlant protease inhibitorshttp://bighost.area.ba.cnr.it/PLANT-PIs
371PlantsP/PlantsTPlant proteins involved in phosphorylation and transporthttp://plantsp.sdsc.edu/
588TIGR plant repeat databaseClassification of repetitive sequences in plant genomeshttp://www.tigr.org/tdb/e2k1/plant.repeats
313TropGENE DBGenes and genomes of sugarcane, banana, cocoahttp://tropgenedb.cirad.fr/
13.2. Arabidopsis thaliana
636AGNSArabidopsis GeneNet supplementary: gene expression and phenotypes of mutants and transgenshttp://emj-pc.ics.uci.edu/mgs/dbases/agns
618AGRISArabidopsis gene regulatory information server: promoters, transcription factors and their target geneshttp://arabidopsis.med.ohio-state.edu/
780Arabidopsis MPSSArabidopsis gene expression detected by massively parallel signature sequencinghttp://mpss.udel.edu/at/
638Arabidopsis Nucleolar Protein DatabaseComparative analysis of human and Arabidopsis nucleolar proteomeshttp://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/proteome_comparison
640ASRPArabidopsis thaliana small RNA projecthttp://cgrb.orst.edu/smallRNA/db/
412ARAMEMNONArabidopsis thaliana membrane proteins and transportershttp://aramemnon.botanik.uni-koeln.de/
765AthaMapGenome-wide map of putative transcription factor binding sites in Arabidopsis thalianahttp://www.athamap.de/
427CATMAComplete Arabidopsis transcriptome microarrayhttp://www.catma.org/
656DATFDatabase of Arabidopsis transcription factorshttp://datf.cbi.pku.edu.cn/
672GabiPDCentral database of the German Plant Genome Projecthttp://gabi.rzpd.de/
675GeneFarmExpert annotation of Arabidopsis gene and protein familieshttp://genoplante-info.infobiogen.fr/Genefarm/
527MAtDBMIPS Arabidopsis thaliana databasehttp://mips.gsf.de/proj/thal/db
738RARGERIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and microarray datahttp://rarge.gsc.riken.jp/
578SeedGenesGenes essential for Arabidopsis developmenthttp://www.seedgenes.org/
97TAIRThe Arabidopsis information resourcehttp://www.arabidopsis.org/
627WAtDBWageningen Arabidopsis thaliana database: mutants, transgenic lines and natural variantshttp://www.watdb.nl/
13.3. Rice
418BGI-RISeBeijing genomics institute rice information systemhttp://rise.genomics.org.cn/
79INEIntegrated rice genome explorerhttp://rgp.dna.affrc.go.jp/giot/INE.html
353IRISInternational rice information systemhttp://www.iris.irri.org/
536MOsDBMIPS Oryza sativa databasehttp://mips.gsf.de/proj/plant/jsf/rice/index.jsp
90OryzabaseRice genetics and genomicshttp://www.shigen.nig.ac.jp/rice/oryzabase/
628Oryza Tag Line databaseT-DNA insertion mutants of ricehttp://genoplante-info.infobiogen.fr/OryzaTagLine/
737RADRice annotation databasehttp://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html
336RiceGAASRice genome automated annotation systemhttp://ricegaas.dna.affrc.go.jp/
569Rice PIPELINEUnification tool for rice databaseshttp://cdna01.dna.affrc.go.jp/PIPE
572Rice proteome databaseRice proteome databasehttp://gene64.dna.affrc.go.jp/RPD/main_en.html
13.4. Other plants
610Brassica ASTRAA database for Brassica genomic researchhttp://hornbill.cspp.latrobe.edu.au/cgi-binpub/index.pl
526MaizeGDBMaize genetics and genomics databasehttp://www.maizegdb.org/
80LIS (formerly MGI)Legume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic datahttp://www.comparative-legumes.org/
539MtDBMedicago trunculata genome databasehttp://www.medicago.org/MtDB
620PoMaMoPotato Maps and More: Potato genome datahttps://gabi.rzpd.de/PoMaMo.html
766SGMDSoybean genomics and microarray databasehttp://psi081.ba.ars.usda.gov/SGMD/default.htm
14. Immunological Databases
642BCIpepA database of B-cell epitopeshttp://bioinformatics.uams.edu/mirror/bcipep/
604dbMHCGenetic and clinical database of the human MHChttp://www.ncbi.nlm.nih.gov/mhc/
150FIMMFunctional molecular immunology datahttp://research.i2r.a-star.edu.sg/fimm
682HaptendbCurated database of hapten moleculeshttp://www.imtech.res.in/raghava/haptendb/
779HLA Ligand/MotifA database and search tool for HLA sequenceshttp://hlaligand.ouhsc.edu/
501IL2RgbaseX-linked severe combined immunodeficiency mutationshttp://research.nhgri.nih.gov/scid/
172IMGTInternational immunogenetics information system: immunoglobulins, T cell receptors, MHC and RPIhttp://imgt.cines.fr/
503IMGT/Gene-DBVertebrate immunoglobulin and T cell receptor geneshttp://imgt.cines.fr/cgi-bin/GENElect.jv
173IMGT/HLAPolymorphism of human MHC and related geneshttp://www.ebi.ac.uk/imgt/hla/
504IMGT/LIGM-DBImmunoglobulin, T cell receptor and MHC nucleotide sequences from human and other vertebrateshttp://imgt.cines.fr/cgi-bin/IMGTlect.jv
16Interferon Stimulated Gene DatabaseGenes induced by treatment with interferonshttp://www.lerner.ccf.org/labs/williams/xchip-html.cgi
692IPD-ESTDABImmunologically characterized melanoma cell lineshttp://www.ebi.ac.uk/ipd/estdab/
693IPD-HPAImmuno polymorphism of human platelet antigenshttp://www.ebi.ac.uk/ipd/hpa/
694IPD-KIRImmuno polymorphism of killer-cell Ig-like receptorshttp://www.ebi.ac.uk/ipd/kir/
691IPD-MHCSequences of the major histocompatibility complexhttp://www.ebi.ac.uk/ipd/mhc/
361JenPepQuantitative binding data for immunological protein–peptide interactionshttp://www.jenner.ac.uk/Jenpep
702MHCBNA database of MHC binding and non-binding peptideshttp://www.imtech.res.in/raghava/mhcbn/
181MHCPEPMHC-binding peptideshttp://wehih.wehi.edu.au/mhcpep/
107MPIDMHC—peptide interaction databasehttp://surya.bic.nus.edu.sg/mpid
621VBASE2Variable genes from the Ig loci of human and mousehttp://www.vbase2.org/

https://www.yeabio.com/pages/distributors


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.