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Bioinformatic Databases 1  

2011-03-28 08:43:48|  分类: Bioinformatics |  标签: |举报 |字号 订阅

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1. Nucleotide Sequence Databases
    1.1. International Nucleotide Sequence Database Collaboration
    1.2. DNA sequences: genes, motifs and regulatory sites
      1.2.1. Coding and coding DNA
      1.2.2. Gene structure, introns and exons, splice sites
      1.2.3. Transcriptional regulator sites and transcription factors
2. RNA sequence databases
3. Protein sequence databases
    3.1. General sequence databases
    3.2. Protein properties
    3.3. Protein localization and targeting
    3.4. Protein sequence motifs and active sites
    3.5. Protein domain databases; protein classification
    3.6. Databases of individual protein families
4. Structure Databases
    4.1. Small molecules
    4.2. Carbohydrates
    4.3. Nucleic acid structure
    4.4. Protein structure
5. Genomics Databases (non-human)
    5.1. Genome annotation terms, ontologies and nomenclature
      5.1.1. Taxonomy and Identification
    5.2. General genomics databases
    5.3. Organism-specific databases
      5.3.1. Viruses
      5.3.2. Prokaryotes
        5.3.2.1. Escherichia coli
        5.3.2.2. Bacillus subtilis
        5.3.2.3. Other bacteria
      5.3.3. Unicellular eukaryotes
      5.3.4. Fungi
        5.3.4.1. Yeasts
        5.3.4.2. Other fungi
      5.3.5. Invertebrates
        5.3.5.1. Caenorhabditis elegans
        5.3.5.2. Drosophila melanogaster
        5.3.5.3. Other invertebrates
6. Metabolic Enzymes and Pathways; Signaling Pathways
    6.1. Enzymes and Enzyme Nomenclature
    6.2. Metabolic Pathways
    6.3. Intermolecular Interactions and Signaling Pathways
7. Human and other Vertebrate Genomes
    7.1. Model organisms, comparative genomics
    7.2. Human genome databases, maps and viewer
    7.3. Human proteins
8. Human Genes and Diseases
    8.1. General Databases
    8.2. Human Mutations Databases
      8.2.1. General polymorphism databases
      8.2.2. Cancer
      8.2.3. Gene-, system- or disease-specific
9. Microarray Data and other Gene Expression Databases
10. Proteomics Resources
11. Other Molecular Biology Databases
    11.1. Drugs and drug design
    11.2. Probes
    11.3. Unclassified databases
12. Organelle Databases
    12.1. Mitochondrial Genes and Proteins
13. Plant Databases
    13.1. General plant databases
    13.2. Arabidopsis thaliana
    13.3. Rice
    13.4. Other plants
14. Immunological Databases 

详细列表


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
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 acidshttp://www.genome.ad.jp/aaindex/
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 pathwayshttp://www.genome.ad.jp/ligand/
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 systemhttp://glycan.genome.ad.jp/
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 anddrug 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 analysishttp://mbgd.genome.ad.jp/
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.http://bacillus.genome.ad.jp/
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 KEGGhttp://www.genome.ad.jp/brite
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







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.


From:http://www.cls.zju.edu.cn/binfo/lecture/2005_spring/databases.html
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