Abbreviations of Genetic Databases

These abbreviations are used in PubMed and refer to Molecular Biology databses.

PCR, qPCR and RT-PCR sequences and primers needed to be alligned through different databses. Today most is done by BLAST on NCBI.

Lieven Gevaert, Bio-ir, RUG 1969

Director Gentaur Database

16S and 23S rRNA Mutation Database16S and 23S ribosomal RNA mutationshttp://www.fandm.edu/Departments/Biology/Databases/RNA.html
16S rRNA databaseMultiple sequence alignment of prokaryotic 16S rDNAhttp://greengenes.llnl.gov/16S/
2D-PAGEProteome database system for microbial researchhttp://www.mpiib-berlin.mpg.de/2D-PAGE
3D-GENOMICSStructural annotations for complete proteomeshttp://www.sbg.bio.ic.ac.uk/3dgenomics
3DID3D interacting domains: Domain-domain interactions in proteins with known 3D structureshttp://3did.embl.de
5S rRNA Database5S rRNA sequenceshttp://biobases.ibch.poznan.pl/5SData/
5’SAGE5′-end serial analysis of gene expressionhttp://5sage.gi.k.u-tokyo.ac.jp/
AAindexPhysicochemical properties of amino acidshttp://www.genome.ad.jp/aaindex/
AANTAmino acid-nucleotide interaction databasehttp://aant.icmb.utexas.edu/
AARSDBAminoacyl-tRNA synthetase databasehttp://rose.man.poznan.pl/aars/index.html
ABAAscidian body atlas: digital 3D model of ascidian developmenthttp://ciona.lab.nig.ac.jp/ascidian_3d_db_demo/ascidian/sample/top.html
ABCdbArchaeal and bacterial ABC transporter databasehttp://www-abcdb.biotoul.fr
ABSAnnotated regulatory binding sites from orthologous promotershttp://genome.imim.es/datasets/abs2005/abs.html
ACeDBC. elegans, S. pombe, and human genomic informationhttp://www.acedb.org/
ACLAMEA classification of genetic mobile elementshttp://aclame.ulb.ac.be/
ACTIVITYFunctional DNA/RNA site activityhttp://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
ADDAA database of protein domain classificationhttp://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
AffinDBAffinity data for protein-ligand complexeshttp://www.agklebe.de/affinity
AGDAshbya gossypii genome databasehttp://agd.unibas.ch
ALFREDAllele frequencies and DNA polymorphismshttp://alfred.med.yale.edu/
AllGenesHuman and mouse gene, transcript and protein annotationhttp://www.allgenes.org/
ALPSbaseAutoimmune lymphoproliferative syndrome databasehttp://research.nhgri.nih.gov/alps/
AluGeneComplete Alu map in the human genomehttp://alugene.tau.ac.il/
AlzGeneCandidate genes for Alzheimer diseasehttp://www.alzgene.org
aMAZEhttp://www.amaze.ulb.ac.be/
Androgen Receptor Gene Mutations DatabaseMutations in the androgen receptor genehttp://www.mcgill.ca/androgendb/
ANTIMICDatabase of natural antimicrobial peptideshttp://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/
AOBaseAntisense oligonucleotide selection and designhttp://www.bioit.org.cn/ao/aobase
APDAntimicrobial peptide databasehttp://aps.unmc.edu/AP/main.php
ApiEST-DBEST sequences from various Apicomplexan parasiteshttp://www.cbil.upenn.edu/paradbs-servlet
AppaDBA database on the nematode Pristionchus pacificushttp://appadb.eb.tuebingen.mpg.de/
Aptamer databaseSmall RNA/DNA molecules binding nucleic acids, proteinshttp://aptamer.icmb.utexas.edu/
ArchDBAutomated classification of protein loop structureshttp://gurion.imim.es/archdb
AREDAU-rich element-containing mRNA databasehttp://rc.kfshrc.edu.sa/ared
ArgonauteGene regulation by mammalian microRNAshttp://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface
ArkDBGenome databases for farm and other animalshttp://www.thearkdb.org/
ArrayExpressPublic collection of microarray gene expression datahttp://www.ebi.ac.uk/arrayexpress
ASAPAlternative spliced isoformshttp://bioinfo.mbi.ucla.edu/ASAP/
ASAPA systematic annotation package for community analysis of E. coli and related genomeshttps://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
ASCActive sequence collection: biologically-active peptideshttp://bioinformatica.isa.cnr.it/ASC/
ASDAlternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdbhttp://www.ebi.ac.uk/asd
ASDBAlternative splicing database: protein products and expression patterns of alternatively-spliced geneshttp://hazelton.lbl.gov/~teplitski/alt
ASHESdbAlternatively spliced human genes by exon skippinghttp://sege.ntu.edu.sg/wester/ashes/
ASPDArtificial selected proteins/peptides databasehttp://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
ASTRALSequences of domains of known structure, selected subsets and sequence-structure correspondenceshttp://astral.stanford.edu/
ATDAlternate transcript diversity databasehttp://www.ebi.ac.uk/atd
Atlas 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/
AxeldbGene expression in Xenopus laevishttp://www.dkfz-heidelberg.de/abt0135/axeldb.htm
BacMapPicture atlas of annotated bacterial genomeshttp://wishart.biology.ualberta.ca/BacMap
BacTregulatorsTranscriptional regulators of AraC and TetR familieshttp://www.bactregulators.org/
BAliBASEA database for comparison of multiple sequence alignmentshttp://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
BayGenomicsGenes relevant to cardiovascular and pulmonary diseasehttp://baygenomics.ucsf.edu/
BeetleBaseGenome database of the beetle Tribolium castaneumhttp://www.bioinformatics.ksu.edu/BeetleBase/
BGEDBrain gene expression databasehttp://genome.mc.pref.osaka.jp/BGED/
BINDhttp://www.bind.ca
BioCartahttp://www.biocarta.com/genes/allPathways.asp
BioCycPathway/genome databases for many bacteriahttp://biocyc.org/
BioGridhttp://biodata.mshri.on.ca/grid
BioImageDatabase of multidimensional biological imageshttp://www.bioimage.org/
BioMagResBankNMR spectroscopic data for proteins and nucleic acidshttp://www.bmrb.wisc.edu/
BioModelsPublished mathematical models of biological interesthttp://www.ebi.ac.uk/biomodels/
BioSilicoIntegrated access to various metabolic databaseshttp://biosilico.kaist.ac.kr/
BIOZONA database of gene and protein familiy classificationhttp://biozon.org
BlocksAlignments of conserved regions in protein familieshttp://blocks.fhcrc.org/
BodyMapHuman and mouse gene expression datahttp://bodymap.ims.u-tokyo.ac.jp/
BodyMap-XsA database for cross-species comparison of vertebrate gene expressionhttp://bodymap.jp/
BRENDAEnzyme names and biochemical propertieshttp://www.brenda.uni-koeln.de
BRITEhttp://www.genome.ad.jp/brite
BSDBiodegradative strain database: Microorganisms that can degrade aromatic and other organic compoundshttp://bsd.cme.msu.edu/
BSORFBacillus subtilis genome database at Kyoto U.http://bacillus.genome.ad.jp/
BTKbaseMutation registry for X-linked agammaglobulinemiahttp://bioinf.uta.fi/BTKbase/
C. elegans ProjectGenome sequencing data at the Sanger Institutehttp://www.sanger.ac.uk/Projects/C_elegans
CADBConformational angles in proteins databasehttp://cluster.physics.iisc.ernet.in/cadb/
CADRECentral Aspergillus data repositoryhttp://www.cadre.man.ac.uk/
CAGECAGE tags for cap-analysis of gene expressionhttp://fantom31p.gsc.riken.jp/cage/mm5/
CampyDBDatabase for Campylobacter genome analysishttp://campy.bham.ac.uk/
Cancer ChromosomesCytogenetic, clinical, and reference information on cancer-related aberrationshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes
Candida GenomeCandida albicans genome databasehttp://www.candidagenome.org/
CandidaDBCandida albicans genome databasehttp://genolist.pasteur.fr/CandidaDB
CarpeDBComprehensive database on the genetics of epilepsyhttp://www.carpedb.ua.edu/
CASRDBCalcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidismhttp://www.casrdb.mcgill.ca/
CATHProtein domain structures databasehttp://www.biochem.ucl.ac.uk/bsm/cath_new
CCDSConsensus CDS: collaborative effort to identify a core set of human protein coding regionshttp://www.ncbi.nlm.nih.gov/projects/CCDS/
CCSDComplex carbohydrate structure database (CarbBank )http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
CDDConserved domain database, includes protein domains from Pfam, SMART, COG and KOG databaseshttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
CE3D protein structure alignmentshttp://cl.sdsc.edu/ce.html
CGEDCancer gene expression databasehttp://cged.hgc.jp
ChEBIChemical entities of biological interesthttp://www.ebi.ac.uk/chebi/
ChickVDSequence variation in the chicken genomehttp://chicken.genomics.org.cn/
ChimerDBPutative chimeric sequences in the GenBankhttp://genome.ewha.ac.kr/ECgene/ChimerSearch/
CIDBChlamydia Interactive Database: Gene expression datahttp://www.it.deakin.edu.au/CIDB
Ciliate IES-MDS DbMacro- and micronuclear genes in spirotrichous ciliateshttp://oxytricha.princeton.edu/dimorphism/database.htm
CisRedHuman regulatory DNA sequence motifshttp://www.cisred.org/
CKAAPs DBStructurally-similar proteins with dissimilar sequenceshttp://ckaap.sdsc.edu/
CleanExExpression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisonshttp://www.cleanex.isb-sib.ch/
ClostriDBFinished and unfinished genomes of Clostridium spp.http://clostri.bham.ac.uk/
CluSTrClusters of Swiss-Prot+TrEMBL proteinshttp://www.ebi.ac.uk/clustr
CnidBaseCnidarian evolution and gene expression databasehttp://cnidbase.bu.edu/
CoCConservation of conservation: Universally conserved residues in selected protein foldshttp://kulibin.mit.edu/coc/
COGClusters of orthologous groups of proteinshttp://www.ncbi.nlm.nih.gov/COG
COGEMEPhytopathogenic fungi and oomycete EST databasehttp://cogeme.ex.ac.uk
CoGenT++Complete genome tracking: Predicted peptides from fully sequenced genomeshttp://cgg.ebi.ac.uk/cogentpp.html
coliBaseA database for E. coli, Salmonella and Shigellahttp://colibase.bham.ac.uk/
ColibriE. coli genome database at Institut Pasteurhttp://genolist.pasteur.fr/Colibri/
Collagen Mutation DatabaseHuman type I and type III collagen gene mutationshttp://www.le.ac.uk/genetics/collagen/
ColumbaAnnotation of protein structures from the PDBhttp://www.columba-db.de
COMeCo-ordination of metals etc.: classification of metalloproteinshttp://www.ebi.ac.uk/come
Comparative GenometricsNucleotide frequencies and the GC and TA skews in complete genome sequenceshttp://www.unil.ch/comparativegenometrics/
CopSComprehensive peptide signature databasehttp://203.90.127.70/copsv2/index.html
CORGComparative regulatory genomics: conserved non-coding sequence blockshttp://corg.molgen.mpg.de/
COSMICCatalogue of somatic mutations in cancer: Sequence data, samples and publicationshttp://www.sanger.ac.uk/perl/CGP/cosmic
Cre Transgenic DatabaseCre transgenic mouse lines with links to publicationshttp://www.mshri.on.ca/nagy/
CroW 21Human chromosome 21 databasehttp://bioinfo.weizmann.ac.il/crow21/
CryptoDBCryptosporidium parvum genome databasehttp://cryptodb.org/
CSACatalytic site atlas: active sites and catalytic residues in enzymes of known 3D structurehttp://www.ebi.ac.uk/thornton-srv/databases/CSA/
CSDCambridge structural database: Crystal structure information for organic and metal-organic compoundshttp://www.ccdc.cam.ac.uk/prods/csd/csd.html
CSDBaseCold shock domain-containing proteinshttp://www.chemie.uni-marburg.de/~csdbase/
CSSCarbohydrate structure suite: carbohydrate 3D structureshttp://www.dkfz.de/spec/css/
CTGAThe catalogue for transmission genetics in Arabshttp://www.cags.org.ae
CUTGCodon usage tabulated from GenBankhttp://www.kazusa.or.jp/codon/
CuticleDBStructural proteins of Arthropod cuticlehttp://bioinformatics.biol.uoa.gr/cuticleDB
CyanoBaseCyanobacterial genomeshttp://www.kazusa.or.jp/cyano
CybaseProteins with cyclic backboneshttp://research.imb.uq.edu.au/cybase/html/index.php
CyberCell databaseA collection of data on E. coli K12 intended for mathematical modeling to simulate the bacterial cellhttp://redpoll.pharmacy.ualberta.ca/CCDB
Cyclonethttp://cyclonet.biouml.org/index.html
CYGDMIPS Comprehensive yeast genome databasehttp://mips.gsf.de/proj/yeast
Cypriot national mutation databaseDisease mutations in the Cypriot populationhttp://www.goldenhelix.org/cypriot/
Cytokine Gene Polymorphism in Human DiseaseCytokine gene polymorphism literature databasehttp://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm
DaliProtein fold classification using the Dali search enginehttp://www.bioinfo.biocenter.helsinki.fi:8080/dali/
DARTDrug adverse reaction target databasehttp://xin.cz3.nus.edu.sg/group/drt/dart.asp
Database nameFull name and/or descriptionURL
Database of Genomic VariantsHuman genomic variants: frequency, segmental duplications and genome assembly gapshttp://projects.tcag.ca/variation/
DBDTranscription factor prediction databasehttp://stash.mrc-lmb.cam.ac.uk/skk/Cell2/index.cgi?Home
dbERGEIIDatabase of experimental results on gene expression: Genomic alignment, annotation and experimental datahttp://dberge.cse.psu.edu/menu.html
dbPTMInformation on post-translational modification of proteinshttp://dbptm.mbc.nctu.edu.tw/
dbQSNPQuantification of SNP allele frequencies databasehttp://qsnp.gen.kyushu-u.ac.jp/
dbRIPHuman retrotransposon insertion polymorphismhttp://falcon.roswellpark.org:9090/
dbSNPDatabase of single nucleotide polymorphismshttp://www.ncbi.nlm.nih.gov/SNP/
DBSubLocDatabase of protein subcellular localizationhttp://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
DBTBSBacillus subtilis promoters and transcription factorshttp://dbtbs.hgc.jp/
DBTGRA database of tunicate (Ciona) gene regulationhttp://dbtgr.hgc.jp/
DCCPDatabase of copper-chelating proteinshttp://sdbi.sdut.edu.cn/DCCP/en/index.php
DDBJ – DNA Data Bank of JapanAll known nucleotide and protein sequenceshttp://www.ddbj.nig.ac.jp
DDIBDatabase of domain interactions and bindinghttp://www.ddib.org/
Decoys ‘R’ UsComputer-generated protein conformationshttp://dd.stanford.edu/
DEDDatabase of evolutionary distanceshttp://warta.bio.psu.edu/DED/
DEGDatabase of essential genes from bacteria and yeasthttp://tubic.tju.edu.cn/deg
DenizBeta-thalassemia allele frequencies in world populationshttp://biobase.fatih.edu.tr/deniz1.html
DExH/D Family DatabaseDEAD-box, DEAH-box and DExH-box proteinshttp://www.helicase.net/dexhd/dbhome.htm
DG-CSTDisease gene conserved sequence tagshttp://143.225.208.11/cst3/
Diatom EST DatabaseESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutumhttp://avesthagen.sznbowler.com/
DictyBaseUniversal resource for Dictyostelium discoideumhttp://dictybase.org/
DIPDatabase of interacting proteins: Experimentally-determined protein-protein interactionshttp://dip.doe-mbi.ucla.edu
DisProtDatabase of Protein Disorder: proteins that lack fixed 3D structure in their native stateshttp://divac.ist.temple.edu/disprot
DMAPSA database of multiple alignments for protein structureshttp://bioinformatics.albany.edu/~dmaps
DomInsDomain insertions in known protein structureshttp://www.domins.org/
DoOPDatabase of orthologous promoters: chordates and plantshttp://doop.abc.hu/
DPDBDrosophila polymorphism databasehttp://dpdb.uab.es/
DPInteractBinding sites for E. coli DNA-binding proteinshttp://arep.med.harvard.edu/dpinteract
DPVwebDescriptions of plant viruseshttp://www.dpvweb.net
DRCDatabase of ribosomal crosslinkshttp://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc
Drosophila microarray projectData and tools for Drosophila gene expression studieshttp://www.flyarrays.com/fruitfly
DrugBankCombined information on drugs and drug targetshttp://redpoll.pharmacy.ualberta.ca/drugbank/
DSDBASENative and modeled disulfide bonds in proteinshttp://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
DSMMDatabase of simulated molecular motionshttp://projects.villa-bosch.de/dbase/dsmm/
DynaProt 2DProteome database of Lactococcus lactishttp://www.wzw.tum.de/proteomik/lactis/
EASEDExtended alternatively spliced EST databasehttp://eased.bioinf.mdc-berlin.de/
EBI GenomesEBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomeshttp://www.ebi.ac.uk/genomes
eBLOCKSHighly conserved protein sequence blockshttp://fold.stanford.edu/eblocks/acsearch.html
ECgeneGenome annotation for alternative splicinghttp://genome.ewha.ac.kr/ECgene/
EchoBASEPost-genomic studies of Escherichia colihttp://www.ecoli-york.org/
EcoCycE. coli K12 genes, metabolic pathways, transporters, and gene regulationhttp://ecocyc.org/
EcoGeneSequence and literature data on E. coli genes and proteinshttp://bmb.med.miami.edu/EcoGene/EcoWeb/
EDASEST-derived alternative splicing databasehttp://www.ig-msk.ru:8005/EDAS/
eF-siteElectrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active siteshttp://ef-site.protein.osaka-u.ac.jp/eF-site
EGOEukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indiceshttp://www.tigr.org/tdb/tgi/ego/
EHCOEncyclopedia of hepatocellular carcinoma genes onlinehttp://ehco.nchc.org.tw
EICO DBExpression-based imprint candidate organiser: a database for discovery of novel imprinted geneshttp://fantom2.gsc.riken.jp/EICODB/
EIDExon-intron databasehttp://www.meduohio.edu/bioinfo/eid/
EMAGEEdinburgh mouse atlas gene expression databasehttp://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html
emap AtlasEdinburgh mouse atlas: a digital atlas of mouse embryo development and spatially-mapped gene expressionhttp://genex.hgu.mrc.ac.uk/
EMBL Nucleotide Sequence DatabaseAll known nucleotide and protein sequenceshttp://www.ebi.ac.uk/embl.html
EMGlibEnhanced microbial genomes library: Completely sequenced genomes of unicellular organismshttp://pbil.univ-lyon1.fr/emglib/emglib.html
eMOTIFProtein sequence motif determination and searcheshttp://motif.stanford.edu/emotif
E-MSDEBI’s macromolecular structure databasehttp://www.ebi.ac.uk/msd
Endogenous GPCR ListG protein-coupled receptors; expression in cell lineshttp://www.tumor-gene.org/GPCR/gpcr.html
EndoNethttp://endonet.bioinf.med.uni-goettingen.de/
EnsemblAnnotated information on eukaryotic genomeshttp://www.ensembl.org/
EnsemblAnnotated information on eukaryotic genomeshttp://www.ensembl.org/
Entrez GeneGene-centered information at NCBIhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Entrez 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
ENZYMEEnzyme nomenclature and propertieshttp://www.expasy.org/enzyme
Enzyme NomenclatureIUBMB Nomenclature Committee recommendationshttp://www.chem.qmw.ac.uk/iubmb/enzyme
EPConDBEndocrine pancreas consortium databasehttp://www.cbil.upenn.edu/EPConDB
EPDEukaryotic promoter databasehttp://www.epd.isb-sib.ch
EpoDBGenes expressed during human erythropoiesishttp://www.cbil.upenn.edu/EpoDB/
ERGDBEstrogen responsive genes databasehttp://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/
ERGOLightIntegrated biochemical data on 9 bacterial genomes: Publicly-available portion of the ERGO databasehttp://www.ergo-light.com/ERGO
EROP-MoscowEndogenous regulatory oligopeptide databasehttp://erop.inbi.ras.ru
Essential genes in E. coliFirst results of an E. coli gene deletion projecthttp://www.genome.wisc.edu/resources/essential.htm
ESTHEREsterases and other alpha/beta hydrolase enzymeshttp://www.ensam.inra.fr/esther
European rRNA databaseAll complete or nearly complete rRNA sequenceshttp://www.psb.ugent.be/rRNA/.
ExIntExon–intron structure of eukaryotic geneshttp://sege.ntu.edu.sg/wester/exint/
EXProtSequences of proteins with experimentally verified functionhttp://www.cmbi.kun.nl/EXProt/
Extra-TRAINExtragenic regions and transcriptional regulators in bacteria and archaeahttp://www.era7.com/ExtraTrain/
EyeSiteFamilies of proteins functioning in the eyehttp://eyesite.cryst.bbk.ac.uk/
EzCatDBEnzyme Catalytic Mechanism Databasehttp://mbs.cbrc.jp/EzCatDB/
FANTOMFunctional annotation of mouse full-length cDNA cloneshttp://fantom3.gsc.riken.jp/
FESDFunctional element SNPs database: SNPs located within promoters, UTRs, etc., of human geneshttp://combio.kribb.re.kr/ksnp/resd/
FGDBMIPS Fusarium graminearum genome databasehttp://mips.gsf.de/genre/proj/fusarium/
FLIGHTInegrated data on Drosophila phenotypes, gene expression and protein interaction datahttp://flight.licr.org/
FlyBaseDrosophila sequences and genomic informationhttp://flybase.bio.indiana.edu/
FlyBrainDatabase of the Drosophila nervous systemhttp://flybrain.neurobio.arizona.edu
FlyMineIntegration of insect genomic and proteomic datahttp://www.flymine.org/
FlyRNAi DRSCGenome-wide RNAi analysis data in Drosophilahttp://flyRNAi.org/cgi-bin/RNAi_screens.pl
FlyTrapDrosophila mutants created using protein trap strategyhttp://flytrap.med.yale.edu/
FlyViewDrosophila development and geneticshttp://pbio07.uni-muenster.de/
FREPFunctional repeats in mouse cDNAshttp://facts.gsc.riken.go.jp/FREP/
FSNFlexible structural neighborhood, structural neighbors of proteins identified by FATCAT toolhttp://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl
Full-MalariaFull-length cDNA library from erythrocytic-stage Plasmodium falciparumhttp://fullmal.ims.u-tokyo.ac.jp/
FUNPEPLow-complexity peptides capable of forming amyloid plaquehttp://www.cmbi.kun.nl/swift/FUNPEP/gergo/
FunShiftFunctional divergence between the subfamilies of a protein domain familyhttp://funshift.cgb.ki.se/
FusionDBDatabase of bacterial and archaeal gene fusion eventshttp://igs-server.cnrs-mrs.fr/FusionDB
GadFlyGenome annotation database of Drosophilahttp://www.fruitfly.org
GALAGenomic alignment, annotation and experimental resultshttp://gala.cse.psu.edu/
GDBHuman genes and genomic mapshttp://www.gdb.org/
GelBank2D gel electrophoresis patterns of proteins from complete microbial genomeshttp://gelbank.anl.gov/
GenAtlasHuman genes, markers and phenotypeshttp://www.genatlas.org/
GenBank®All known nucleotide and protein sequenceshttp://www.ncbi.nlm.nih.gov/Entrez
GenDiSGenomic distribution of protein structural superfamilieshttp://caps.ncbs.res.in/gendis/home.html
Gene Resource LocatorAlignment of ESTs with finished human sequencehttp://grl.gi.k.u-tokyo.ac.jp/
Gene3DPrecalculated structural assignments for whole genomeshttp://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
GeneAnnotRevised annotation of Affymetrix human gene probe setshttp://genecards.weizmann.ac.il/geneannot/
GeneCardsIntegrated database of human genes, maps, proteins and diseaseshttp://bioinfo.weizmann.ac.il/cards/
GeneDBCurated database for various Sanger-sequenced genomeshttp://www.genedb.org/
GeneLocGene location databasehttp://genecards.weizmann.ac.il/geneloc/
GeneNestGene indices of human, mouse, zebrafish, etc.http://genenest.molgen.mpg.de/
GeneNethttp://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet
GeneNoteHuman genes expression profiles in healthy tissueshttp://genecards.weizmann.ac.il/genenote/
GenePaintGene expression patterns in the mousehttp://www.genepaint.org/Frameset.html
Genetic CodesGenetic codes in various organisms and organelleshttp://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
GeneTideA transcriptome-focused member of the GeneCards suitehttp://genecards.weizmann.ac.il/genetide/
GeneTrapExpression patterns in an embryonic stem library of gene trap insertionshttp://www.cmhd.ca/genetrap/
GenewHuman gene nomenclature: approved gene symbolshttp://www.gene.ucl.ac.uk/nomenclature
GeniSysEnhancer- and promoter-inserted mutants of Drosophilahttp://genisys.kaist.ac.kr:8080/
GenMapDBMapped human BAC cloneshttp://genomics.med.upenn.edu/genmapdb
GenoBaseE. coli genome database at Nara Institutehttp://ecoli.aist-nara.ac.jp/
GénolevuresA comparison of S. cerevisiae and 14 other yeast specieshttp://cbi.labri.fr/Genolevures
Genome AtlasDNA structural properties of sequenced genomeshttp://www.cbs.dtu.dk/services/GenomeAtlas/
Genome Information BrokerDDBJ’s collection of genome databaseshttp://gib.genes.nig.ac.jp
Genome ReviewsIntegrated view of complete genomeshttp://www.ebi.ac.uk/GenomeReviews/
GenProtECE. coli K12 genome and proteome databasehttp://genprotec.mbl.edu
GENSATGene expression nervous system atlas: a map of gene expression in the central nervous system of the mousehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat
GEOGene expression omnibus: Gene expression profileshttp://www.ncbi.nlm.nih.gov/geo/
Germline p53 MutationsMutations in human tumor and cell line p53 genehttp://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm
GermOnlineGene expression in mitotic and meiotic cell cyclehttp://www.germonline.org/
GLIDAG-protein coupled receptors ligand databasehttp://gdds.pharm.kyoto-u.ac.jp:8081/glida/
GlycanCarbohydrate database, part of the KEGG systemhttp://glycan.genome.ad.jp/
GlycoSuiteDBN- and O-linked glycan structures and biological sourceshttps://tmat.proteomesystems.com/glycosuite/
GOGene ontology consortium databasehttp://www.geneontology.org/
GOAEBI’s gene ontology annotation projecthttp://www.ebi.ac.uk/GOA
GOLDGenomes online database: a listing of completed and ongoing genome projectshttp://www.genomesonline.org/
GOLD.dbGenomics of lipid-associated disorders databasehttp://gold.tugraz.at
GPCRDBG protein-coupled receptors databasehttp://www.gpcr.org/7tm/
gpDBG-proteins and their interaction with GPCRshttp://bioinformatics.biol.uoa.gr/gpDB
GRAPMutants of G-protein coupled receptors of family Ahttp://tinygrap.uit.no/GRAP/
GRSDBG-rich sequences databasehttp://bioinformatics.ramapo.edu/grsdb/
GTDGenomic threading database: Structural annotations of complete proteomeshttp://bioinf.cs.ucl.ac.uk/GTD
GTOPProtein fold predictions from genome sequenceshttp://spock.genes.nig.ac.jp/~genome/
GtRDBGenomic tRNA databasehttp://lowelab.ucsc.edu/GtRNAdb/
Guide RNA DatabaseRNA editing in various kinetoplastid specieshttp://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
GXDMouse gene expression databasehttp://www.informatics.jax.org/menus/expression_menu.shtml
HaemBFactor IX gene mutations, insertions and deletionshttp://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html
HAGRHuman ageing genomic resources: Genes related to ageing in humans and model organismshttp://genomics.senescence.info/
H-ANGELHuman anatomic gene expression libraryhttp://www.jbirc.aist.go.jp/hinv/index.jsp
HbVarHuman hemoglobin variants and thalassemiashttp://globin.cse.psu.edu/globin/hbvar
HCADHuman chromosome aberration database: Chromosomal breakpoints and affected geneshttp://www.pdg.cnb.uam.es/UniPub/HCAD/
HCVDBThe hepatitis C virus databasehttp://hepatitis.ibcp.fr/
HemBaseGenes expressed in differentiating human erythroid cellshttp://hembase.niddk.nih.gov/
HemoPDBHematopoietic promoter databasehttp://bioinformatics.med.ohio-state.edu/HemoPDB
HERVdHuman endogenous retrovirus databasehttp://herv.img.cas.cz
Het-PDB NaviHetero-atoms in protein structureshttp://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
HGMDHuman gene mutation databasehttp://www.hgmd.org/
HGT-DBPutative horizontally-transferred genes in prokaryotic genomeshttp://www.fut.es/~debb/HGT/
HGVbaseHuman genome variation database: Curated human polymorphismshttp://hgvbase.cgb.ki.se/
HGVS DatabasesA compilation of human mutation databaseshttp://www.hgvs.org/
HIC-UpHetero-compound Information Centre – Uppsalahttp://xray.bmc.uu.se/hicup
H-InvDBFull-length human cDNA cloneshttp://www.h-invitational.jp/
Histone DatabaseHistone fold sequences and structureshttp://research.nhgri.nih.gov/histones/
HitsA database of protein domains and motifshttp://hits.isb-sib.ch/
HIV Drug Resistance DatabaseHIV mutations that confer resistance to anti-HIV drugshttp://resdb.lanl.gov/Resist_DB/default.htm
HIV Molecular Immunology DatabaseHIV epitopeshttp://hiv-web.lanl.gov/immunology/
HIV RT and Protease Sequence DatabaseHIV reverse transcriptase and protease sequenceshttp://hivdb.stanford.edu/
HIV Sequence DatabaseHIV RNA sequenceshttp://hiv-web.lanl.gov/
HollywoodExon annotation databasehttp://hollywood.mit.edu
Homeobox PageHomeobox proteins, classification and evolutionhttp://www.biosci.ki.se/groups/tbu/homeo.html
Homeodomain ResourceHomeodomain sequences, structures and related genetic and genomic informationhttp://research.nhgri.nih.gov/homeodomain/
HomoloGeneAutomatically detected homologous genes in complete eukaryotic genomeshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
HomophilaDrosophila homologs of human disease genes tohttp://superfly.ucsd.edu/homophila/
HOMSTRADHomologous structure alignment database: curated structure-based alignments for protein familieshttp://www-cryst.bioc.cam.ac.uk/homstrad
HoppsigenHuman and mouse homologous processed pseudogeneshttp://pbil.univ-lyon1.fr/databases/hoppsigen.html
HORDEHuman olfactory receptor data exploratoriumhttp://bioinfo.weizmann.ac.il/HORDE/
HOWDYHuman organized whole genome databasehttp://www-alis.tokyo.jst.go.jp/HOWDY/
Hox-ProHomeobox genes databasehttp://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
hp-DPIDatabase of protein interactions in Helicobacter pylorihttp://dpi.nhri.org.tw/hp/
HPIDHuman protein interaction databasehttp://www.hpid.org/
HPMRHuman plasma membrane receptome: sequences, literature, and expression datahttp://receptome.stanford.edu/
HPRDHuman protein reference database: domain architecture, post-translational modifications, and disease associationhttp://www.hprd.org
HPTAAHuman potential tumor-associated antigenshttp://www.bioinfo.org.cn/hptaa/
HS3DHomo sapiens splice sites datasethttp://www.sci.unisannio.it/docenti/rampone/
HTPSELEXTranscription factor binding site sequences obtained using high-throughput SELEX methodhttp://www.isrec.isb-sib.ch/htpselex/
HUGEHuman unidentified gene-encoded large (>50 kDa) protein and cDNA sequenceshttp://www.kazusa.or.jp/huge
HugeIndexExpression levels of human genes in normal tissueshttp://zlab.bu.edu/HugeSearch
HuGeMapHuman genome genetic and physical map datahttp://www.infobiogen.fr/services/Hugemap
Human BAC EndsNon-redundant human BAC end sequenceshttp://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
Human Genome Segmental Duplication DatabaseSegmental duplications in the human genomehttp://projects.tcag.ca/humandup
Human 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
Human PAX2 Allelic Variant DatabaseMutations in human PAX2 genehttp://pax2.hgu.mrc.ac.uk/
Human PAX6 Allelic Variant DatabaseMutations in human PAX6 genehttp://pax6.hgu.mrc.ac.uk/
HumHotHuman meiotic recombination hot spotshttp://www.jncasr.ac.in/humhot/
HUNTHuman novel transcripts: annotated full-length cDNAshttp://www.hri.co.jp/HUNT
HuSiDaHuman siRNA databasehttp://itb1.biologie.hu-berlin.de/~nebulus/sirna/
HyPaLibHybrid pattern library: structural elements in classes of RNAhttp://bibiserv.techfak.uni-bielefeld.de/HyPa/
IARC TP53 DatabaseHuman TP53 somatic and germline mutationshttp://www-p53.iarc.fr/index.html
ICBgyrB database for identification of bacteriahttp://seasquirt.mbio.co.jp/icb/index.php
ICDSInterrupted coding sequences – frameshifts, stop codons, sequencing errors in microbial genomeshttp://www-bio3d-igbmc.u-strasbg.fr/ICDS/
IGTCInternational mouse Gene Trap Consortium datahttp://wwwtest.genetrap.org
IMB Jena Image LibraryVisualization and analysis of 3D biopolymer structureshttp://www.imb-jena.de/IMAGE.html
IMGIntergrated microbial genome database at the DOE Joint Genome Institutehttp://img.jgi.doe.gov/
IMGT/3Dstructure-DBSequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteinshttp://imgt3d.igh.cnrs.fr/
IMGT/PRIMER-DBImmunogenetics oligonucleotide primer databasehttp://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl
IMOTdbSpatially interacting motif databasehttp://caps.ncbs.res.in/imotdb/
Imprinted Gene CatalogueImprinted genes and parent-of-origin effects in animalshttp://igc.otago.ac.nz/home.html
InBaseInteins (protein splicing elements) database: properties, sequences, bibliographyhttp://www.neb.com/neb/inteins.html
INFEVERSHereditary inflammatory disorder and familial mediterranean fever mutation datahttp://fmf.igh.cnrs.fr/infevers
Influenza Virus ResourceProtein and nucleotide sequences of the influenza virushttp://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
InparanoidA database of eukaryotic orthologshttp://inparanoid.cgb.ki.se/
InsulatorDBInsulator regulatory elements in vertebrate genomeshttp://insulatordb.utmem.edu
IntAct projectProtein-protein interaction datahttp://www.ebi.ac.uk/intact
Integr8Functional classification of proteins in whole genomeshttp://www.ebi.ac.uk/integr8/
IntEnzIntegrated enzyme database and enzyme nomenclaturehttp://www.ebi.ac.uk/intenz
InterActive FlyDrosophila genes and their roles in developmenthttp://flybase.bio.indiana.edu/allied-data/lk/interactive-fly/aimain/1aahome.htm
Inter-Chain Beta-SheetsProtein-protein interactions mediated by interchain beta-sheet formationhttp://www.igb.uci.edu/servers/icbs/
InterDomPutative protein domain interactionshttp://interdom.lit.org.sg
InterProIntegrated resource of protein families, domains and functional siteshttp://www.ebi.ac.uk/interpro
IntroneratorAlternative splicing in C. elegans and C. briggsaehttp://www.cse.ucsc.edu/~kent/intronerator/
IntroneratorIntrons and splicing in C. elegans and C. briggsaehttp://www.cse.ucsc.edu/~kent/intronerator/
INVHOGENHomologous invertebrate geneshttp://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html
IPDImmuno polymorphism databasehttp://www.ebi.ac.uk/ipd
IPIInternational protein index: human, mouse and rat proteinshttp://www.ebi.ac.uk/IPI
iProClassIntegrated protein classification databasehttp://pir.georgetown.edu/iproclass/
iProClassProtein families defined by PIR superfamilies and PROSITE patternshttp://pir.georgetown.edu/gfserver/proclass.html
IRESdbInternal ribosome entry site databasehttp://ifr31w3.toulouse.inserm.fr/IRESdatabase/
IRESiteExperimentally studied internal ribosome entry siteshttp://www.iresite.org/
ISfinderInsertion sequences from bacteria and archaeahttp://www-is.biotoul.fr
IslanderPathogenicity islands and prophages in bacterial genomeshttp://www.indiana.edu/~islander
ISSDIntegrated sequence-structure databasehttp://www.protein.bio.msu.su/issd
ITTACAIntegrated tumor transcriptome array and clinical data analysishttp://bioinfo.curie.fr/ittaca
IUBMB Nomenclature databaseNomenclature of enzymes, membrane transporters, electron transport proteins and other proteinshttp://www.chem.qmul.ac.uk/iubmb
IUPAC Nomenclature databaseNomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commissionhttp://www.chem.qmul.ac.uk/iupac
IUPHAR-RDInternational Union of Pharmacology recommendations on receptor nomenclature and drug classificationhttp://www.iuphar-db.org/iuphar-rd/
IXDBPhysical maps of human chromosome Xhttp://ixdb.mpimg-berlin-dahlem.mpg.de/
JASPARPSSMs for transcription factor DNA-binding siteshttp://jaspar.cgb.ki.se
JSNPJapanese SNP databasehttp://snp.ims.u-tokyo.ac.jp/
KaryotypeDBKaryotype and chromosome data for animal and plant specieshttp://www.nenno.it/karyotypedb/
KDBIKinetic data of bio-molecular interactionshttp://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php
KEGGKyoto encyclopedia of genes and genomes: databases on genes, proteins, and metabolic pathwayshttp://www.genome.jp/kegg
KEGG PathwayMetabolic and regulatory pathways in complete genomeshttp://www.genome.jp/kegg/pathway.html
Kidney Development DatabaseKidney development and gene expressionhttp://golgi.ana.ed.ac.uk/kidhome.html
KinG – Kinases in GenomesS/T/Y-specific protein kinases encoded in complete genomeshttp://hodgkin.mbu.iisc.ernet.in/~king
KinMutBaseDisease-causing protein kinase mutationshttp://www.uta.fi/imt/bioinfo/KinMutBase/
KlothoCollection and categorization of biological compoundshttp://www.biocheminfo.org/klotho
KnottinsDatabase of knottins – small proteins with an unusual “disulfide through disulfide” knothttp://knottin.cbs.cnrs.fr
KOGEukaryotic orthologous groups of proteinshttp://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi
L1BaseFunctional annotation and prediction of LINE-1 elementshttp://line1.molgen.mpg.de/
LEGERPost-genome research of Listeriahttp://leger2.gbf.de/cgi-bin/expLeger.pl
LeptoListLeptospira interrogans genomehttp://bioinfo.hku.hk/LeptoList
LGICdbLigand-gated ion channel subunit sequences databasehttp://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
LIFEdbLocalization, interaction and functions of human proteinshttp://www.dkfz.de/LIFEdb
LIGANDChemical compounds and reactions in biological pathwayshttp://www.genome.ad.jp/ligand/
Lipase Engineering DatabaseSequence, structure and function of lipases and esteraseshttp://www.led.uni-stuttgart.de/
Lipid MAPSLipid metabolites and pathways strategyhttp://www.lipidmaps.org
LOCATEMembrane organization and subcellular localization of mouse proteinshttp://mpdb.imb.uq.edu.au
LOLAList of lists annotated: a comparison of gene sets identified in different microarray experimentshttp://www.lola.gwu.edu/
Lowe Syndrome Mutation DatabaseMutations causing Lowe oculocerebrorenal syndromehttp://research.nhgri.nih.gov/lowe/
LOX-DBMammalian, invertebrate, plant and fungal lipoxygenaseshttp://www.dkfz-heidelberg.de/spec/lox-db/
LPFCLibrary of protein family core structureshttp://www-smi.stanford.edu/projects/helix/LPFC
LumbriBASEESTs of the earthworm Lumbricus rubellushttp://www.earthworms.org/
MACiEMechanism, annotation and classification in enzymes: enzyme reaction mechanismshttp://www-mitchell.ch.cam.ac.uk/macie/
MAGESTAscidian (Halocynthia roretzi) gene expression patternshttp://www.genome.ad.jp/magest
MAMEPMolecular anatomy of the mouse embryo project: Gene expression data on mouse embryoshttp://mamep.molgen.mpg.de/
Map ViewerDisplay of genomic information by chromosomal positionhttp://www.ncbi.nlm.nih.gov/mapview/
MAPPERPutative transcription factor binding sites in various genomeshttp://bio.chip.org/mapper
MBGDMicrobial genome database for comparative analysishttp://mbgd.genome.ad.jp/
MeGXMarine ecological genomix: genomics and metagenomics of marine bacteriahttp://www.Megx.net
MEPDMedaka (freshwater fish Oryzias latipes) gene expression pattern databasehttp://www.embl.de/mepd/
MeRNAMetal ion binding sites in RNAhttp://merna.lbl.gov
MEROPSDatabase of proteolytic enzymes (peptidases)http://merops.sanger.ac.uk/
MetaCycMetabolic pathways and enzymes from various organismshttp://metacyc.org
MetaGrowthGrowth requirements of bacterial pathogenshttp://igs-server.cnrs-mrs.fr/axenic/
Metalloprotein SiteMetal-binding sites in metalloproteinshttp://metallo.scripps.edu/
MetaRouterCompounds and pathways related to bioremediationhttp://pdg.cnb.uam.es/MetaRouter
MethDBDNA methylation data, patterns and profileshttp://www.methdb.de/
MFunGDMIPS mouse functional genomics databasehttp://mips.gsf.de/genre/proj/mfungd
MGCMammalian genome collection: Full-length ORFs for human, mouse, and rat geneshttp://mgc.nci.nih.gov/
MICdbProkaryotic microsatelliteshttp://www.cdfd.org.in/micas
microRNA RegistryDatabase of microRNAs (small noncoding RNAs)http://www.sanger.ac.uk/Software/Rfam/mirna/
MIPSProtein databases at Munich Information Center for Protein Sequenceshttp://mips.gsf.de/
miRNAMapmicroRNA precursors and their mapping to targets in vertebrate genomeshttp://mirnamap.mbc.nctu.edu.tw
MMDBNCBI’s database of 3D structures, part of NCBI Entrezhttp://www.ncbi.nlm.nih.gov/Structure
MNCDBMIPS Neurospora crassa databasehttp://mips.gsf.de/proj/neurospora/
Mobile group II intronsA database of group II introns, self-splicing catalytic RNAshttp://www.fp.ucalgary.ca/group2introns/
ModBaseAnnotated comparative protein structure modelshttp://salilab.org/modbase
MODOMICSA database of RNA modification pathwayshttp://genesilico.pl/modomics/
MolliGenGenomic data on mollicuteshttp://cbi.labri.fr/outils/molligen/
MolMovDBDatabase of macromolecular movements: Descriptions of protein and macromolecular motions, including movieshttp://bioinfo.mbb.yale.edu/MolMovDB/
Monosaccharide BrowserSpace-filling Fischer projections of monosaccharideshttp://www.beechtreecommon.org/biochemistry/monosaccharide/
Mouse Genome InformaticsFormerly mouse genome databasehttp://www.informatics.jax.org/
Mouse SAGESAGE libraries from various mouse tissues and cell lineshttp://mouse.biomed.cas.cz/sage
MpactYeast protein-protein interaction datahttp://mips.gsf.de/genre/proj/mpact
MPDBSynthetic oligonucleotides useful as primers or probeshttp://www.biotech.ist.unige.it/interlab/mpdb.html
MPromDBMammalian promoter databasehttp://bioinformatics.med.ohio-state.edu/MPromDb
MTBMouse tumor biology database: Tumor types, genes, classification, incidence, pathologyhttp://tumor.informatics.jax.org/
MtbRegListMycobacterium tuberculosis gene regulationhttp://www.USherbrooke.ca/vers/MtbRegList
MTIDMouse transposon insertion databasehttp://mouse.ccgb.umn.edu/transposon/
MulPSSMMultiple PSSMs of structural and sequence familieshttp://hodgkin.mbu.iisc.ernet.in/~mulpssm
NASCarraysNottingham Arabidopsis Stock Centre microarray databasehttp://affymetrix.arabidopsis.info
NCBI Protein databaseAll protein sequences: translated from GenBank and imported from other protein databaseshttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
NCBI RefSeqNon-redundant collection of naturally-occurring biological moleculeshttp://www.ncbi.nlm.nih.gov/RefSeq/
NCBI TaxonomyNames of all organisms represented in GenBankhttp://www.ncbi.nlm.nih.gov/Taxonomy/
NCBI Viral GenomesViral genome resource at NCBIhttp://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html
NCIRNon-canonical interactions in RNA structureshttp://prion.bchs.uh.edu/bp_type/
NCL Mutation DatabasePolymorphisms in neuronal ceroid lipofuscinoses geneshttp://www.ucl.ac.uk/ncl/
ncRNAs DatabaseNon-coding RNAs with regulatory functionshttp://biobases.ibch.poznan.pl/ncRNA/
NDBNucleic acid-containing structureshttp://ndbserver.rutgers.edu/
NegProtNegative Proteome: A tool for comparison of complete proteomeshttp://superfly.ucsd.edu/negprot
Nematode.netParasitic nematode sequencing projecthttp://nematode.net/
NEMBASENematode sequence and functional data databasehttp://www.nematodes.org/
NESbaseNuclear export signals databasehttp://www.cbs.dtu.dk/databases/NESbase
NetAffxPublic Affymetrix probesets and annotationshttp://www.affymetrix.com/
NLSdbNuclear localization signalshttp://cubic.bioc.columbia.edu/db/NLSdb/
NMPdbNuclear matrix associated proteins databasehttp://www.rostlab.org/db/NMPdb/
NONCODEA database of noncoding RNAshttp://www.bioinfo.org.cn/NONCODE/index.htm
NOPdbNucleolar proteome databasehttp://www.lamondlab.com/NOPdb/
NPDNuclear protein databasehttp://npd.hgu.mrc.ac.uk/
NPInterNoncoding RNA-protein interactionshttp://www.bioinfo.org.cn/NPInter
NPRDNucleosome positioning region databasehttp://srs6.bionet.nsc.ru/srs6/
NRSubNon-redundant Bacillus subtilis database at U. Lyonhttp://pbil.univ-lyon1.fr/nrsub/nrsub.html
NTDBThermodynamic data for nucleic acidshttp://ntdb.chem.cuhk.edu.hk/
Nuclear Receptor ResourceNuclear receptor superfamilyhttp://nrr.georgetown.edu/NRR/nrrhome.htm
NucleaRDBNuclear receptor superfamilyhttp://www.receptors.org/NR/
NUREBASENuclear hormone receptors databasehttp://www.ens-lyon.fr/LBMC/laudet/nurebase.html
NURSANuclear receptor signaling atlashttp://www.nursa.org
ODBOperon databasehttp://odb.kuicr.kyoto-u.ac.jp/
OGDOomycete Genomics Database: ESTs and annotationhttp://www.oomycete.net/
O-GlycBaseO- and C-linked glycosylation sites in proteinshttp://www.cbs.dtu.dk/databases/OGLYCBASE/
Olfactory Receptor DatabaseSequences for olfactory receptor-like moleculeshttp://senselab.med.yale.edu/senselab/ordb/
OMIAOnline Mendelian inheritance in animals: A catalog of animal genetic and genomic disordershttp://www.angis.org.au/omia
OMIMOnline Mendelian inheritance in man: A catalog of human genetic and genomic disordershttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
OncoMineCancer microarray data by gene or cancer typehttp://www.oncomine.org/
ooTFDObject-oriented transcription factors databasehttp://www.ifti.org/ootfd
Open Proteomics DatabaseMass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacteriumhttp://bioinformatics.icmb.utexas.edu/OPD/
OPHIDOnline predicted human interaction databasehttp://ophid.utoronto.ca
Oral Cancer Gene DatabaseCellular and molecular data for genes involved in oral cancerhttp://www.tumor-gene.org/Oral/index.html
ORFanageDatabase of orphan ORFs (ORFs with no homologs) in complete microbial genomeshttp://www.cs.bgu.ac.il/~nomsiew/ORFans
ORFDBCollection of ORFs that are sold by Invitrogenhttp://orf.invitrogen.com/
OrthoMCLOrthologous protein clusters from multiple genomeshttp://orthomcl.cbil.upenn.edu
Osteo-Promoter DatabaseGenes in osteogenic proliferation and differentiationhttp://www.opd.tau.ac.il
PACRATArchaeal and bacterial intergenic sequence featureshttp://www.biosci.ohio-tate.edu/~pacrat
PA-GOSUBProtein sequences from model organisms, GO assignment and subcellular localizationhttp://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
PAHdbMutations at the phenylalanine hydroxylase locushttp://www.mcgill.ca/pahdb/
PALIPhylogeny and alignment of homologous protein structureshttp://pauling.mbu.iisc.ernet.in/~pali
PANDITProtein and associated nucleotide domains with inferred treeshttp://www.ebi.ac.uk/goldman-srv/pandit/
PANTHERGene products organized by biological functionhttp://panther.celera.com/
ParaDBParalogy mapping in human genomeshttp://abi.marseille.inserm.fr/paradb/
PartiGeneDBAssembled partial genomes for ~250 eukaryotic organismshttp://www.partigenedb.org/
PASS2Structural motifs of protein superfamilieshttp://ncbs.res.in/~faculty/mini/campass/pass.html
PathBaseEuropean mutant mice histopathology database: imageshttp://www.pathbase.net/
PathDBBiochemical pathways, compounds and metabolismhttp://www.ncgr.org/pathdb
PathguideA listing of pathway, signal transduction and protein-protein interaction databaseshttp://pathguide.org
PDBProtein structure databank: all publicly available 3D structures of proteins and nucleic acidshttp://www.rcsb.org/pdb
PDB_TMTransmembrane proteins with known 3D structurehttp://pdbtm.enzim.hu/
PDB-Ligand3D structures of small molecules bound to proteins and nucleic acidshttp://www.idrtech.com/PDB-Ligand/
PDB-REPRDBRepresentative protein chains, based on PDB entrieshttp://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
PDBrtfRepresentation of target families of enzymes in PDBhttp://cgl.imim.es/pdbrtf/
PDBSite3D structure of protein functional siteshttp://srs6.bionet.nsc.ru/srs6/
PDBsumSummaries and analyses of PDB structureshttp://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
PDZBaseProtein-protein interactions involving PDZ domainshttp://icb.med.cornell.edu/services/pdz/start
PECProfiling of E. coli chromosomehttp://shigen.lab.nig.ac.jp/ecoli/pec
PEDANTResults of an automated analysis of genomic sequenceshttp://pedant.gsf.de/
PEDBProstate expression database: ESTs from prostate tissue and cell type-specific cDNA librarieshttp://www.pedb.org/
PEDEPig EST data explorer: full-length cDNAs and ESTshttp://pede.gene.staff.or.jp/
PEPPredictions for entire proteomes: Summarized analyses of protein sequenceshttp://cubic.bioc.columbia.edu/pep/
PepConfDBA database of peptide conformationshttp://www.peptidome.org/products/list.htm
PEPRPublic expression profiling resource: Expression profiles in a variety of diseases and conditionshttp://pepr.cnmcresearch.org
PepSeekerPeptide identification and ion information from proteome experimentshttp://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl
PeptaibolPeptaibol (antibiotic peptide) sequenceshttp://www.cryst.bbk.ac.uk/peptaibol/welcome.html
PeptideAtlasPeptides identified in LC-MS/MS proteomics experimentshttp://www.peptideatlas.org
PfamProtein families: Multiple sequence alignments and profile hidden Markov models of protein domainshttp://www.sanger.ac.uk/Software/Pfam/
PGDBProstate and prostatic diseases gene databasehttp://www.ucsf.edu/pgdb/
PGTdbProkaryotic growth temperature databasehttp://pgtdb.csie.ncu.edu.tw/
PharmGKBPharmacogenomics knowledge base: effect of genetic variation on drug responseshttp://www.pharmgkb.org/
PhenomicDBComparison of phenotypes of orthologous genes in human and model organismshttp://www.phenomicdb.de/
PHEXdbPHEX mutations causing X-linked hypophosphatemiahttp://www.phexdb.mcgill.ca/
PHI-baseGenes affecting fungal pathogen-host interactionshttp://www4.rothamsted.bbsrc.ac.uk/phibase/
Phospho.ELMS/T/Y protein phosphorylation sites (former PhosphoBase)http://phospho.elm.eu.org/
Phytophthora Functional Genomics DatabaseESTs and expression data from P. infestans and P. sojaehttp://www.pfgd.org/pfgd/
PINdbProteins interacting in nucleus (human and yeast)http://pin.mskcc.org/
PINTProtein-protein interactions thermodynamic databasehttp://pintdb.dyndns.org/index.html
PIR-ALNCurated database of protein sequence alignmentshttp://pir.georgetown.edu/pirwww/dbinfo/piraln.html
PIR-NREFPIR’s non-redundant reference protein databasehttp://pir.georgetown.edu/pirwww/pirnref.shtml
PIRSFFamily/superfamily classification of whole proteinshttp://pir.georgetown.edu/pirsf/
PKRProtein kinase resource: sequences, enzymology, genetics and molecular and structural propertieshttp://pkr.sdsc.edu/html/index.shtml
PLACEPlant cis-acting regulatory DNA elementshttp://www.dna.affrc.go.jp/htdocs/PLACE
Plant snoRNA DBsnoRNA genes in plant specieshttp://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
PlantCAREPlant promoters and cis-acting regulatory elementshttp://intra.psb.ugent.be:8080/PlantCARE/
PLANTncRNAsPlant non-coding RNAshttp://www.prl.msu.edu/PLANTncRNAs
PlantPromPlant promoter sequences for RNA polymerase IIhttp://mendel.cs.rhul.ac.uk/
PlasmoDBPlasmodium genome databasehttp://plasmodb.org/
PLPMDBPyridoxal-5′-phosphate dependent enzymes mutationshttp://www.studiofmp.com/plpmdb/
PMDCompilation of protein mutant datahttp://pmd.ddbj.nig.ac.jp/
PMDB3D protein models obtained from structure predictionshttp://a.caspur.it/PMDB/
POINTPrediction of human protein-protein interactomehttp://point.nchc.org.tw/
PolyA_DBA database of mammalian mRNA polyadenylationhttp://polya.umdnj.edu/polyadb/
PolymorphixA database of sequence polymorphismshttp://pbil.univ-lyon1.fr/polymorphix/query.php
Poxvirus.orgPoxvirus genomic sequences and gene annotationhttp://www.poxvirus.org/
PPDProtein pKa databasehttp://www.jenner.ac.uk/ppd/
PPNEMAPlant-parasitic nematode rRNAshttp://bighost.area.ba.cnr.it/PPNEMA/
PRECISEPredicted and consensus interaction sites in enzymeshttp://precise.bu.edu/precisedb/
PRFProtein research foundation database of peptides: sequences, literature and unnatural amino acidshttp://www.prf.or.jp/en
PRIDEProteomics identification databasehttp://www.ebi.ac.uk/pride/
PrimerPCRPCR primers for eukaryotic and prokaryotic geneshttp://bioinfo.ebc.ee/PrimerStudio/
PRINTSHierarchical gene family fingerprintshttp://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
probeBaserRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated informationhttp://www.microbial-ecology.net/probebase
ProDomProtein domain familieshttp://www.toulouse.inra.fr/prodom.html
PRODORICProkaryotic database of gene regulation networkshttp://prodoric.tu-bs.de/
ProLysEDA database of bacterial protease systemshttp://genome.ukm.my/prolyses/
ProlysisProteases and natural and synthetic protease inhibitorshttp://delphi.phys.univ-tours.fr/Prolysis/
PromECE. coli promoters with experimentally-identified transcriptional start siteshttp://margalit.huji.ac.il/promec/
PROMISEProsthetic centers and metal ions in protein active siteshttp://metallo.scripps.edu/PROMISE
ProNITThermodynamic data on protein-nucleic acid interactionshttp://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
PROPHECYProfiling of phenotypic characteristics in yeasthttp://prophecy.lundberg.gu.se/
ProRuleFunctional and structural information on PROSITE profileshttp://www.expasy.org/tools/scanprosite
PROSITEBiologically-significant protein patterns and profileshttp://www.expasy.org/prosite
Protein Folding DatabaseExperimental data on protein foldinghttp://pfd.med.monash.edu.au
Protein-protein interfacesInteracting residues in protein-protein interfaces in PDBhttp://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
ProTeusSignature sequences at the protein N- and C-terminihttp://www.proteus.cs.huji.ac.il/
ProThermThermodynamic data for wild-type and mutant proteinshttp://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
ProtoMapHierarchical classification of Swiss-Prot proteinshttp://protomap.cornell.edu/
ProtoNetHierarchical clustering of Swiss-Prot proteinshttp://www.protonet.cs.huji.ac.il/
PseudoBaseDatabase of RNA pseudoknotshttp://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
PseudoCAPPseudomonas aeruginosa genome database and community annotation projecthttp://www.pseudomonas.com/
PSIbaseInteraction of proteins with known 3D structureshttp://psimap.kaist.ac.kr/
PSORTdbProtein subcellular localization in bacteriahttp://db.psort.org/
pSTIINGProtein signalling, transcriptional interactions and inflammation networks gatewayhttp://pstiing.licr.org/
PTCH1 Mutation DatabaseMutations and SNPs found in PTCH1 genehttp://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html
PubChemStructures and biological activities of small organic moleculeshttp://pubchem.ncbi.nlm.nih.gov/
PubMedCitations and abstracts of biomedical literaturehttp://pubmed.gov/
PUMA2Metabolic analysis of complete microbial genomeshttp://compbio.mcs.anl.gov/puma2
QPPDQuantitative PCR Primer Database for human and mousehttp://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp
QTL MatchmakerQuantitative trait loci mapping in human, mouse and rathttp://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
Rat Genome DatabaseRat genetic and genomic datahttp://rgd.mcw.edu/
RatMapRat genome tools and datahttp://ratmap.org/
RB1 Gene Mutation DBMutations in the human retinoblastoma (RB1) genehttp://www.d-lohmann.de/Rb/
RDP-IIRibosomal database projecthttp://rdp.cme.msu.edu
Reactomehttp://www.reactome.org/
REBASERestriction enzymes and associated methylaseshttp://rebase.neb.com/rebase/rebase.html
RECODEGenes using programmed translational recoding in their expressionhttp://recode.genetics.utah.edu/
RefExAReference database for human gene expression analysishttp://www.lsbm.org/db/index_e.html
REFOLDExperimental data on protein refolding and purificationhttp://refold.med.monash.edu.au
RegulonDBTranscriptional regulation and operon organization in E.colihttp://www.cifn.unam.mx/Computational_Genomics/regulondb/
RESIDPre-, co- and post-translational protein modificationshttp://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html
RfamNon-coding RNA familieshttp://www.sanger.ac.uk/Software/Rfam/
RHdbRadiation hybrid map datahttp://www.ebi.ac.uk/RHdb
Ribonuclease P DatabaseRNase P sequences, alignments and structureshttp://www.mbio.ncsu.edu/RNaseP/home.html
RIDOMrRNA-based differentiation of medical microorganismshttp://www.ridom-rdna.de/
RISSCRibosomal internal spacer sequence collectionhttp://ulises.umh.es/RISSC
RNA Modification DatabaseNaturally modified nucleosides in RNAhttp://medlib.med.utah.edu/RNAmods/
RNA SSTRANDRNA secondary structure data and structural motifshttp://www.rnasoft.ca/sstrand/
RNABaseRNA-containing structures from PDB and NDBhttp://www.rnabase.org/
RNAdbMammalian noncoding RNA databasehttp://ncrna.bioinformatics.com.au/
RNAi codexClones from mouse, human and rat shRNA librarieshttp://codex.cshl.org
RNAiDBRNAi phenotypic analysis of C. elegans geneshttp://www.rnai.org/
RNRdbRibonucleotide reductase databasehttp://rnrdb.molbio.su.se/
rOGEDRat ovarian gene expression databasehttp://app.mc.uky.edu/kolab/rogedendo.aspx
ROSPathhttp://rospath.ewha.ac.kr/
RPGRibosomal protein gene databasehttp://ribosome.miyazaki-med.ac.jp/
RRNDBrRNA operon numbers in various prokaryoteshttp://rrndb.cme.msu.edu/
RsGDBRhodobacter sphaeroides genomehttp://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/
rSNP GuideSNPs in regulatory gene regionshttp://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
RTCGDMouse retroviral tagged cancer gene databasehttp://rtcgd.ncifcrf.gov/
RTKdbReceptor tyrosine kinase sequenceshttp://pbil.univ-lyon1.fr/RTKdb/
RTPrimerDBReal-time PCR primer and probe sequenceshttp://medgen.ugent.be/rtprimerdb/
S/MARt dBNuclear scaffold/matrix attached regionshttp://smartdb.bioinf.med.uni-goettingen.de/
S4Structure-based sequence alignments of SCOP superfamilieshttp://compbio.mds.qmw.ac.uk/~james/S4.shtml
SAGEmapNCBI’s resource for SAGE data from various organismshttp://www.ncbi.nlm.nih.gov/SAGE
SARS-CoV RNA SSSPredicted secondary structures of SARS coronavirus RNAhttp://www.liuweibo.com/sarsdb/
SBASEProtein domain sequences and toolshttp://www.icgeb.org/sbase
SCAdbSpinocerebellar ataxia candidate gene databasehttp://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map
SCMDSaccharomyces cerevisiae morphological database: micrographs of budding yeast mutantshttp://yeast.gi.k.u-tokyo.ac.jp/
SCOPStructural classification of proteinshttp://scop.mrc-lmb.cam.ac.uk/scop
SCOPECMapping of catalytic function to domain structurehttp://www.enzome.com/databases/scopec.php
SCOPPIStructural classification of protein-protein interfaceshttp://www.scoppi.org
SCORStructural classification of RNA: RNA motifs by structure, function and tertiary interactionshttp://scor.lbl.gov/
ScorpionDatabase of scorpion toxinshttp://research.i2r.a-star.edu.sg:8080/scorpion/
SCPDSaccharomyces cerevisiae promoter databasehttp://rulai.cshl.edu/SCPD/
SDAPStructural database of allergenic proteins and food allergenshttp://fermi.utmb.edu/SDAP
SELEX_DBDNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichmenthttp://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
SENTRASensory signal transduction proteinshttp://compbio.mcs.anl.gov/sentra/
SEVENS7-transmembrane helix receptors (G-protein-coupled)http://sevens.cbrc.jp/
SGCEdbStructural genomics of C. eleganshttp://sgce.cbse.uab.edu/
SGDSaccharomyces genome databasehttp://www.yeastgenome.org/
ShiBaseShigella databasehttp://www.mgc.ac.cn/ShiBASE/
SIDDBaseStress-induced DNA duplex destabilization profiles of complete microbial genomeshttp://www.genomecenter.ucdavis.edu/benham/siddbase
SIEGESmoking Induced Epithelial Gene Expressionhttp://pulm.bumc.bu.edu/siegeDB
SilkDBSilkworm Bombyx mori ESTs, mutants, photographshttp://www.ab.a.u-tokyo.ac.jp/genome/
SilkSatDbA microsatellite database of the silkworm Bombyx morihttp://210.212.212.7:9999/PHP/SILKSAT/index.php
SIMAPSimilarity matrix of proteins: precomputed similarity datahttp://mips.gsf.de/services/analysis/simap/
siRNAdbFunctional human siRNA sequenceshttp://sirna.cgb.ki.se/
SitesBaseKnown ligand binding sites in the PDBhttp://www.bioinformatics.leeds.ac.uk/sb/
SKY/M-FISH and CGHFluorescent images of chromosomes and cytogenetic datahttp://www.ncbi.nlm.nih.gov/sky/
SloopClassification of protein loopshttp://www-cryst.bioc.cam.ac.uk/~sloop/
Small RNA DatabaseSmall RNAs from prokaryotes and eukaryoteshttp://condor.bcm.tmc.edu/smallRNA/smallrna.html
SMARTSimple modular architecture research tool: signalling, extracellular and chromatin-associated protein domainshttp://smart.embl-heidelberg.de/
snoRNA-LBME-dbHuman C/D box and H/ACA modification guide RNAshttp://www-snorna.biotoul.fr/
SNP Consortium databaseSNP Consortium datahttp://snp.cshl.org/
SNP500CancerRe-sequenced SNPs from 102 reference sampleshttp://snp500cancer.nci.nih.gov
SNPeffectPhenotypic effects of human coding SNPshttp://snpeffect.vub.ac.be/database.php
SOURCEFunctional genomics resource for human, mouse and rathttp://source.stanford.edu/
SPDSecreted protein databasehttp://spd.cbi.pku.edu.cn
SpliceDBCanonical and non-canonical mammalian splice siteshttp://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb
SpliceInfoModes of alternative splicing in human genomehttp://spliceinfo.mbc.nctu.edu.tw/
SpliceNestA tool for visualizing splicing of genes from EST datahttp://splicenest.molgen.mpg.de/
SpodoBaseGenomics of the butterfly Spodoptera frugiperdahttp://bioweb.ensam.inra.fr/spodobase/
SRPDBSignal recognition particle databasehttp://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
SRPDBProteins of the signal recognition particleshttp://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
SSU rRNA Modification DatabaseModified nucleosides in small subunit rRNAhttp://medstat.med.utah.edu/SSUmods/
STACKSequence tag alignment and consensus knowledgebasehttp://www.sanbi.ac.za/Dbases.html
Stanford Microarray DatabaseRaw and normalized data from microarray experimentshttp://genome-www.stanford.edu/microarray
STCDBhttp://bibiserv.techfak.uni-bielefeld.de/stcdb/
StellaBaseNematostella vectensis (sea anemone) genomehttp://stellabase.org.
STING reportAmino acid properties in proteins of known structurehttp://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/
STRBaseShort tandem DNA repeats databasehttp://www.cstl.nist.gov/div831/strbase/
STRINGPredicted functional associations between proteinshttp://string.embl.de/
Structure Superposition DatabasePairwise superposition of TIM-barrel structureshttp://ssd.rbvi.ucsf.edu/
SubtiListBacillus subtilis genome database at Institut Pasteurhttp://genolist.pasteur.fr/SubtiList/
Subviral RNA DatabaseViroids and viroid-like RNAshttp://subviral.med.uottawa.ca/
SuperDrug2D and 3D chemical structures of various drugshttp://bioinformatics.charite.de/superdrug
SUPERFAMILYAssignments of proteins to structural superfamilieshttp://supfam.org/
SuperNaturalNatural compounds and their suppliershttp://bioinformatics.charite.de/supernatural
SUPFAMGrouping of sequence families into superfamilieshttp://pauling.mbu.iisc.ernet.in/~supfam
SURFACESurface residues and functions annotated, compared and evaluated: a database of protein surface patcheshttp://cbm.bio.uniroma2.it/surface
SV40 Large T-Antigen MutantsMutations in SV40 large tumor antigen genehttp://supernova.bio.pitt.edu/pipaslab/
SWEET-DBAnnotated carbohydrate structure and substance informationhttp://www.dkfz-heidelberg.de/spec2/sweetdb/
SWISS-2DPAGEAnnotated 2D gel electrophoresis databasehttp://www.expasy.org/ch2d/
SWISS-MODEL RepositoryDatabase of annotated 3D protein structure modelshttp://swissmodel.expasy.org/repository
Swiss-ProtNow UniProt/SwissProt, part of the UniProt knowledgebasehttp://www.expasy.org/sprot
SynDBSynaptic protein databasehttp://syndb.cbi.pku.edu.cn
SYSTERSSystematic re-searching and clustering of proteinshttp://systers.molgen.mpg.de/
T1DbaseA resource for type 1 diabetes researchhttp://t1dbase.org/
T4-like genome databaseSequences of T4-like bacteriophages from various sourceshttp://phage.bioc.tulane.edu/
TAEDThe adaptive evolution database: A phylogeny-based tool for comparative genomicshttp://www.bioinfo.no/tools/TAED
TargetDBTarget data from worldwide structural genomics projectshttp://targetdb.pdb.org/
TBestDBTaxonomically broad EST database: protist ESTshttp://tbestdb.bcm.umontreal.ca/searches/welcome.php
TCDBTransporter protein classification databasehttp://www.tcdb.org/
TcruziDBTrypanosoma cruzi genome databasehttp://tcruzidb.org/
TECRdbThermodynamics of enzyme-catalyzed reactionshttp://xpdb.nist.gov/enzyme_thermodynamics/
TESSTranscription element search systemhttp://www.cbil.upenn.edu/tess
TGDTetrahymena thermophila genome databasewww.ciliate.org
The Autism Chromosome Rearrangement DatabaseCurated collection of genomic features related to autismhttp://projects.tcag.ca/autism
The Chromosome 7 Annotation ProjectHuman chromosome 7 sequence and annotationhttp://www.chr7.org/
The Lafora DatabaseMutations and polymorphisms associated with Lafora progressive myoclonus epilepsyhttp://projects.tcag.ca/lafora/
THGSTransmembrane helices in genome sequenceshttp://pranag.physics.iisc.ernet.in/thgs/
TIGR Comprehensive Microbial ResourceVarious data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteinshttp://www.tigr.org/CMR
TIGR Gene IndicesOrganism-specific databases of EST and gene sequenceshttp://www.tigr.org/tdb/tgi.shtml
TIGR Gene IndicesOrganism-specific databases of EST and gene sequenceshttp://www.tigr.org/tdb/tgi.shtml
TIGR Microbial DatabaseLists of completed and ongoing genome projects with links to complete genome sequenceshttp://www.tigr.org/tdb/mdb/mdbcomplete.html
TIGRFAMsTIGR protein families adapted for functional annotationhttp://www.tigr.org/TIGRFAMs
TiProDTissue-specific promoter databasehttp://tiprod.cbi.pku.edu.cn:8080/index.html
TmaDBTissue microarray databasehttp://www.bioinformatics.leeds.ac.uk/tmadb/
TMPDBExperimentally-characterized transmembrane topologieshttp://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
tmRDBtmRNA databasehttp://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
tmRNA WebsitetmRNA sequences and alignmentshttp://www.indiana.edu/~tmrna
Tooth Development DatabaseGene expression in dental tissuehttp://bite-it.helsinki.fi/
TopoSNPTopographic database of non-synonymous SNPshttp://gila.bioengr.uic.edu/snp/toposnp
TOPSTopology of protein structures databasehttp://www.tops.leeds.ac.uk
ToxoDBToxoplasma gondii genome databasehttp://toxodb.org/
TPMDTaiwan polymorphic microsatellite marker databasehttp://tpmd.nhri.org.tw/
TRACTOR dbTranscription factors in gamma-proteobacteria databasehttp://www.tractor.lncc.br/
TRANSCompel®Composite regulatory elements affecting gene transcription in eukaryoteshttp://www.gene-regulation.com/pub/databases.html#transcompel
TRANSFAC®Transcription factors and binding siteshttp://transfac.gbf.de/TRANSFAC/index.html
TRANSPATHhttp://www.biobase.de/pages/products/databases.html
TransportDBPredicted membrane transporters in complete genomes, classified according to the TC classification systemhttp://www.membranetransport.org/
TranstermCodon usage, start and stop signalshttp://guinevere.otago.ac.nz/transterm.html
TRBaseTandem repeats in the human genomehttp://bioinfo.ex.ac.uk/trbase
TREDTranscriptional regulatory element databasehttp://rulai.cshl.edu/tred
Tree of LifeInformation on phylogeny and biodiversityhttp://phylogeny.arizona.edu/tree/phylogeny.html
TreeBasePhylogenetic trees and the data matrices used to generate themhttp://www.treebase.org/
TreeFamTree families database: phylogenetic trees of animal geneshttp://www.treefam.org
T-REGsA list of TGFbeta-responsive geneshttp://actin.ucd.ie/tgfbeta
TrEMBLNow UniProt/TrEMBL, part of the UniProt knowledgebasehttp://www.expasy.org/sprot
TRIPLESTransposon-insertion phenotypes, localization, and expression in Saccharomyceshttp://ygac.med.yale.edu/triples/
tRNA sequencestRNA viewer and sequence editorhttp://www.uni-bayreuth.de/departments/biochemie/trna/
trome, trEST and trGEN:Databases of predicted human protein sequencesftp://ftp.isrec.isb-sib.ch/pub/databases/
TRRDTranscription regulatory regions of eukaryotic geneshttp://www.bionet.nsc.ru/trrd/
TrSDBTranscription factor databasehttp://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
TTDTherapeutic target databasehttp://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp
Tumor Gene Family DatabasesCellular, molecular and biological data about genes involved in various cancershttp://www.tumor-gene.org/tgdf.html
UCSC Archaeal Genome BrowserPyrococcus furiosus genome browserhttp://archaea.ucsc.edu/
UCSC Genome BrowserGenome assemblies and annotationhttp://genome.ucsc.edu/
U-genomeGenome organization in unicellular eukaryoteshttp://sege.ntu.edu.sg/wester/ugenome/
UM-BBDUniversity of Minnesota biocatalysis and biodegradation databasehttp://umbbd.ahc.umn.edu/
UMLSUnified medical language systemhttp://umlsks.nlm.nih.gov/
UniGeneNon-redundant set of eukaryotic gene-oriented clustershttp://www.ncbi.nlm.nih.gov/UniGene/
UniGeneUnified clusters of ESTs and full-length mRNA sequenceshttp://www.ncbi.nlm.nih.gov/UniGene/
UniParcUniProt archive, a repository of all protein sequenceshttp://www.uniprot.org/database/archive.shtml
UniProtUniversal protein knowledgebasehttp://www.uniprot.org/
UniRefClustered sets of related sequences from UniProthttp://www.uniprot.org/database/nref.shtml
UniSTSUnified view of sequence tagged sites with mapping datahttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
UniVecVector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contaminationhttp://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
UTRdb/UTRsite5′- and 3′-UTRs of eukaryotic mRNAshttp://bighost.area.ba.cnr.it/BIG/UTRHome/
VectorDBCharacterization and classification of nucleic acid vectorshttp://genome-www2.stanford.edu/vectordb/
VEGAVertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequenceshttp://vega.sanger.ac.uk/
VIDAHomologous viral protein families databasehttp://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
VIPERdbVirus particle explorer: Virus capsid structureshttp://viperdb.scripps.edu/
Viral Bioinformatics Resource CenterVirus orthologous genes, gene families and genomeshttp://www.virology.ca/
VirFactBacterial virulence factors and pathogenicity islandshttp://virfact.burnham.org/
VirOligoVirus-specific oligonucleotides for PCR and hybridizationhttp://viroligo.okstate.edu/
Virulence FactorsReference database for microbial virulence factorshttp://zdsys.chgb.org.cn/VFs/main.htm
VKCDBVoltage-gated potassium channel databasehttp://vkcdb.biology.ualberta.ca/
VMDVirginia Bioinformatics Institute microbial databasehttp://phytophthora.vbi.vt.edu
WILMAC. elegans annotation databasehttp://www.came.sbg.ac.at/wilma/
Wnt DatabaseWnt proteins and phenotypeshttp://www.stanford.edu/~rnusse/wntwindow.html
WorfDBC. elegans ORFeomehttp://worfdb.dfci.harvard.edu/
WormBaseData repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathwayshttp://www.wormbase.org/
XproEukaryotic protein-encoding DNA sequences, both intron-containing and intron-less geneshttp://origin.bic.nus.edu.sg/xpro/
YDPMYeast deletion project and mitochondria databasehttp://www-deletion.stanford.edu/YDPM/YDPM_index.html
Yeast Intron DatabaseAres lab database of splicesomal introns in S. cerevisiaehttp://www.cse.ucsc.edu/research/compbio/yeast_ introns.html
Yeast snoRNA DatabaseYeast small nucleolar RNAshttp://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
YEASTRACTYeast search for transcriptional regulators and consensus trackinghttp://www.yeastract.com
YGOBYeast gene order browserhttp://wolfe.gen.tcd.ie/ygob
yMGVYeast microarray global viewerhttp://www.transcriptome.ens.fr/ymgv/
YRC PDRYeast resource center public data repositoryhttp://www.yeastrc.org/pdr/
ZFINZebrafish information networkhttp://zfin.org/