生物信息学相关数据库资源介绍.ppt

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1、生物信息学相关数据库资源介绍 Still waters run deep.流静水深流静水深,人静心深人静心深 Where there is life,there is hope。有生命必有希望。有生命必有希望生物信息学相关数据库资源生物信息学相关数据库资源1.核酸及其相关数据库（序列数据库、基因组相关数据库、核酸三维结构数据库、其他）2.蛋白质相关数据库（序列数据库、蛋白质三维结构数据库、蛋白质组数据库（二维凝胶电泳数据库）、信号传导及蛋白质-蛋白质相互作用相关数据库、DNA和蛋白质相互作用数据库）3.基因或蛋白质一些特定数据库4.糖类及其相关数据库5.蛋白质翻译后修饰相关数据库6.基因表达数

2、据库7.人类基因突变及疾病相关数据库8.进化相关数据库及资源专利数据库9.资源目录服务器或网页1.核酸及其相关数据库（序列数据库、基因组相关数据库、核酸三维结构数据库、其他）2.蛋白质相关数据库（序列数据库、蛋白质三维结构数据库、蛋白质组数据库（二维凝胶电泳数据库）、信号传导及蛋白质-蛋白质相互作用相关数据库、DNA和蛋白质相互作用数据库）3.基因或蛋白质一些特定数据库4.糖类及其相关数据库5.蛋白质翻译后修饰相关数据库6.基因表达数据库7.人类基因突变及疾病相关数据库8.进化相关数据库及资源专利数据库9.资源目录服务器或网页核酸及其相关数据库核酸及其相关数据库1）、核酸序列数据库）、核酸序列

3、数据库lBIOSINO我国的核酸序列公共数据库lEMBL-EMBLNucleotidesequencedatabase(EBI)lGenBank-GenBankNucleotideSequencedatabase(NCBI)lDDBJ-DNADataBankofJapanldbEST-DatabaseofExpressedSequenceTags（表达序列标签）(NCBI)ldbSTS-DatabaseofSequenceTaggedSites（序列标签位点）(NCBI)2）.基因组及相关数据库GenomicDatabaseslGenomeWeb(HGMP)-Acatalogueofusefu

4、lWebsitesforGenomicswithasetofcollectionsofgenomedatabaseslGSDB-GenomeSequencedatabase(NCGR)lGOLD-GenomesOn-linedbl一些数据库的直接链接3）.核酸三维结构数据库lNDB-NucleicAcidDatabank(3Dstructures)lBNASDB-NucleicacidstructuredbfromUniversityofPune4）.其他lAsDb-AberrantSplicingdb（异常拼接）（异常拼接）lACUTS-Ancientconserveduntranslate

5、dDNAsequencesdblCodonUsageDb-ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.lEPD-EukaryoticPromoterdb（真核启动子）（真核启动子）lHOVERGEN-HomologousVertebrateGenesdb（同源（同源脊椎动物）脊椎动物）lIMGT-ImMunoGeneTicsdbMirroratEBI（免疫遗传学免疫遗传学）lISIS-IntronSequenceandInformationSystemlRDP-Ribosomal

6、dbProjectlgRNAsdb-GuideRNAdblPLACE-Plantcis-actingregulatoryDNAelementsdb5）其它）其它核酸数据库lPlantCARE-Plantcis-actingregulatoryDNAelementsdblsRNAdb-SmallRNAdblssurRNA-SmallribosomalsubunitdbllsurRNA-Largeribosomalsubunitdbl5SrRNA-5SribosomalRNAdbltmRNAWebsiteltmRDB-tmRNAdBltRNA-tRNAcompilation（编辑）（编辑）from

7、theUniversityofBayreuthluRNADB-uRNAdb5）其他）其他核酸数据库lRNAediting-RNAeditingsitelRNAmoddb-RNAmodificationdblTelDB-MultimediaTelomere（端粒）ResourcelTRADAT-TRAnscriptionDatabasesandAnalysisToolslSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)（类病毒）5）Transgenics（转基因）lCreTransgenicDatabase-Cretransgenic

8、mouselineslTransgenic/TargetedMutationDatabase-Informationontransgenicanimalsandtargetedmutations2.蛋白质序列和相关数据库蛋白质序列数据库蛋白质序列数据库lPIR-international-TheProteinInformationResource(proteinsequence)（国际蛋白质信息中心，（国际蛋白质信息中心，NBRF+JIPID+MIPs,PIR1PIR2PIR3PIR4)）lSWISS-PROT-SWISS-PROTannotated（注释）proteinsequencedb(

9、SIB+EBI,EBI创建蛋白质专家分析系统ExPASy，北京)lMIPS(Munichinformationcenterforproteinsequence)（德国慕尼黑蛋白质序列信息中心德国慕尼黑蛋白质序列信息中心）蛋白质相关数据库蛋白质相关数据库lPROSITE-PROSITEdictionaryofproteinsitesandpatternslInterPro-IntegratedResourcesofProteinsDomainsandFunctionalSiteslBLOCKS-BLOCKSdblDOMO-Proteindomaindb(Automaticallygenerate

10、d)lPfam-Proteinfamiliesdb(HMMderived)MirroratSangerlPRINTS-ProteinMotiffingerprintdblProDom-Proteindomaindb(Automaticallygenerated)lPROTOMAP-Anautomatichierarchical（分等级）（分等级）classificationofSWISS-PROTproteinslSBASE-SBASEdomaindb(Proteindomainsequencelibrary)lSMART-Proteinsignallingandextracellulardo

11、mainpatterns(SimpleModularArchitectureResearchTool)lProClass-Proteinsequencealignmentsandcurationofproteinfamilies蛋白质三维结构和相关数据库蛋白质三维结构和相关数据库lPDB-ProteinDataBankMirrorsinEBIlBioMagResBankRepository（知识）（知识）fordataonproteins,peptides,andnucleicacidsfromNMRspectroscopy（光谱学）（光谱学）lSWISS-MODELRepository-Au

12、tomaticallygeneratedproteinmodelsdblModBase-DbofcomparativeproteinstructuremodelslCATH-UCLBSMstructuralclassificationofproteinslSCOP-StructuralclassificationofproteinsMirroratUSA|Israel|Singapore|AustralialMol_R_Us-MoleculesRUs,browserforPDBlBMMDomainServer-BiomolecularModellingLaboratory(ICRF)prote

13、indomainserverlPRESAGE-Collaborativeresourceforstructuralgenomics蛋白质三维结构和相关数据库蛋白质三维结构和相关数据库 lSBASE-SBASEdomaindb(Proteindomainsequencelibrary)lSMART-Proteinsignallingandextracellular（细胞外）（细胞外）domainpatterns(SimpleModularArchitectureResearchTool)lProClass-Proteinsequencealignmentsandcurationofprotein

14、familieslKabat-KabatdbofproteinofimmunologicalinterestlPMD-ProteinMutantdb蛋白质二维凝胶电泳数据库蛋白质二维凝胶电泳数据库lWORLD-2DPAGE-Acompleteindexof2D-PAGEdbandserverslPhoretixlinks-Phoretixpageoflinksto2Dgeldb3、信号传导及蛋白质、信号传导及蛋白质-蛋白质相互作蛋白质相互作用相关数据库用相关数据库lDIP-DbofInteractingProteinslINTERACT-Protein-Proteininteractiondb

15、lProNet-Protein-ProteininteractiondblCANSITE-SignalTransductions（信号传导）（信号传导）WeblSPAD-SignalingpathwaydblCSNDB-CellSignalingNetworksdbDNA和蛋白质相互作用数据库和蛋白质相互作用数据库lDPInteract-DNA-Proteinsinteractionsdb特定基因或蛋白质的数据库特定基因或蛋白质的数据库lAAA-AAAfamilyofATPasesserverAcetylcholinesteraseslALDH-Aldehydedehydrogenase（醛脱

16、氢酶，l醛氧化酶）genesuperfamilydblAminoacyl-tRNAsynthetasesinSWISS-PROT-Listofaminoacyl-tRNAsynthetasesinSWISS-PROTlAARSDB-Aminoacyl-tRNAsynthetasesdblAllergensinSWISS-PROT-Nomenclatureandindex（命名和索引）ofallergens（过敏原）inSWISS-PROT特定基因或蛋白质的数据库特定基因或蛋白质的数据库lAMSDb-Antimicrobialsequencesdb（抗菌）lAntibodyresourcepag

17、e-LinkstoantibodyrelatedWebresources（抗体）lAustralianvenomandtoxindb（澳大利亚蛇毒）lBacillusthuringiensistoxinspecificitydb（Bt）lTFII-Basaltranscriptionfactors（转录子）lBloodgroupantigensinSWISS-PROT（血型抗原）血型抗原）lBCGD-BreastcancergenesdbfromMBCR（乳癌）lBRENDA-Dbofenzymefunctionaldata特定基因或蛋白质的数据库特定基因或蛋白质的数据库lEF-handCaB

18、P-EF-handcalcium-bindingproteinsdblCAZy-Carbohydrate-ActiveenZYmesWebsitelCBSdomainCystathionine（胱硫醚,丙氨酸丁氨酸硫醚）BetaSynthasedomainWWWpagelCDantigensinSWISS-PROT-Nomenclatureforsurfaceproteinsofhumanleucocytes(白血球CD)特定基因或蛋白质的数据库特定基因或蛋白质的数据库lCDantigensinPROW-DatabaseoninformationaboutCDantigenslChaperon

19、in-InformationonGroELandGroESchaperoninslConotoxins-InformationonconotoxinsfromaWebsiteonconeshellsl。etc。4、糖类相关数据库、糖类相关数据库lCarbBank-ComplexCarbohydrateStructureDatabaselGlycoSuiteDB-DbofglycanstructureslTGN-TheGlycoscienceNetworklFCCA-ForumCarbohydratesComingofAgelCARBHYD-CarbohydrateinformationWWWs

20、iteslMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides（单糖）5、蛋白质翻译后修饰相关数据库、蛋白质翻译后修饰相关数据库lO-GlycBase-O-glycosylated（使(蛋白质)糖基化）proteinsdblPhosphoBase-Phosphorylation（磷酸化作用)sitesdblRESID-DbofAminoAcidModifications6、基因表达数据库基因表达数据库lASDB-Proteinproductsandexpressionpatternsofalternativel

21、y-splicedgeneslAxeldb-GeneexpressioninXenopuslBodyMap-HumanandmousegeneexpressiondatalEpoDB-GenesexpressedinvertebrateRBClFlyView-Drosophiladevelopmentandgenetics（果蝇）lGeneExpressionDatabase(GXD)-Mousegeneexpressionandgenomics（鼠）lKidneyDevelopmentDatabaseKidney（肾）developmentandgeneexpression6、基因表达数据库

22、、基因表达数据库lMAGEST-Ascidian(Halocynthiaroretzi)geneexpressionpatternslMouseAtlasandGeneExpressionDatabase-Spatially-mappedgeneexpressiondatalPEDB-Normalandaberrantprostate（正常、异常前列腺）geneexpressionlToothDevelopmentDatabase-GeneexpressionindentaltissuelTRIPLES-TRansposon-InsertionPhenotypes,Localizationan

23、dExpressioninSaccharomyces（酵母）7、人类基因突变及疾病相关数据库、人类基因突变及疾病相关数据库lHMGD-HumanGeneMutationdblSVD-SequencevariationdblHGBASE-HumanGenicBi-AllelicSequencesdblTheSNPconsortiumldbSNP-Humansinglenucleotidepolymorphism(SNP)db（单核苷酸多态性数据库）lListofmutationdatabasesfromOMIMlListofmutationdatabasesfromIMT(Finland)人类基

24、因突变及疾病相关数据库人类基因突变及疾病相关数据库lADB-Albinismdb(Mutationsinhumangenescausingalbinism（白化病）)lAlpha-glucosidase-Informationabouthumanacidalpha-glucosidase(GSD-II)lARmutations-HumanandrogenreceptormutationdblAntithrombinmutationdb（抗凝血突变）lAsthmaandAllergygenedb（哮喘和过敏）lBIOMDB-Dbofmutationscausingtetrahydrobiopte

25、rindeficiencies（缺乏四氢生物蝶呤缺乏四氢生物蝶呤lBLMbase-HumanBLMmutationdb(Bloomsnydrom)7、人类基因突变及疾病相关数据库、人类基因突变及疾病相关数据库lBTKbase-HumanBTKmutationdb(X-linkedagammaglobulinemia)（血中丙球蛋白贫乏）lCD40Lbase-HumanCD40ligandmutationdblCOL1/3mutation-HumanTypeIandIIIcollagenmutationdblCFTRmutation-Humancysticfibrosismutationdb(C

26、FTR)（囊肿性纤维化，属遗传性胰腺病囊肿性纤维化，属遗传性胰腺病）lEMDdb-HumanEmerin(EMD)mutationdb(Emery-Dreifussmusculardystrophy)肌肉萎缩症肌肉萎缩症lKMeyeDB-Eyediseasegenesdb人类基因突变及疾病相关数据库人类基因突变及疾病相关数据库lFVIImutation-HumanFactorVIImutationdblHAMSTeRS-HumanFactorVIIImutationdb(HaemophiliaA)lHAeMB-HumanFactorIXmutationdb(HaemophiliaB)血友病lF

27、BN1mutation-Humanfibrillin1mutationdb(Marfansyndrome)lG6PD-HumanG6PDdeficiencyresourcelGaltmutation-Humangalactose-1-phosphateuridylyltransferasemutationdb(Galactosemia)人类基因突变及疾病相关数据库人类基因突变及疾病相关数据库lHEXAdb-HumanHexosaminidaseAmutationdb(Tay-sachsdisease)lIL2RGbase-HumanIL2RG(Interleukin-2receptorgamm

28、a)mutationdb(X-SCID)lL1CAMmutation-HumanL1CAMmutationdblLDLRmutation-HumanLDLRmutationdb(Familialhypercholesterolemia)lLQTSdb-LongQTsyndromedblNCF1base-HumanNCF1mutationdblNCF2base-HumanNCF2mutationdb人类基因突变及疾病相关数据库人类基因突变及疾病相关数据库lNeuromusculardiseaseswebsitelNCL-NeuronalCeroidLipofuscinosesmutationdb

29、lOTCase-Humanornithinetranscarbamylase(OTCase)websitelCytochromeP450allelesnomenclaturelp53mutationdb-UniversityofTokyop53mutationdblGermlinep53mutationdb-UniversityofPraguedbofgermlinep53mutationslPAHdb-Humanphenylalaninehydroxylase(PAH)mutationdb人类基因突变及疾病相关数据库人类基因突变及疾病相关数据库lPAX6mutation-HumanPAX6m

30、utationdblPrion-PrionandpriondiseasewebsitelRAG1base-HumanRAG1mutationdblRAG2base-HumanRAG2mutationdblRB1base-Humanretinoblastoma-associatedprotein(RB)mutationdblRetNet-RetinalInformationNetworklRetinaInternationalScientificNewsletter-InformationonRetinalgenes,proteinsanddiseases人类基因突变及疾病相关数据库人类基因突变

31、及疾病相关数据库lTSC-TSC(TSC1/TSC2)variationdblTSC2-Cardiff-RotterdamTuberousSclerosis(TS)db(Tuberin;TSC2)lTGDB-TumorgenedblVMD2mutation-HumanVMD2mutationdblvWFmutation-HumanvonWillebrandfactor(vWF)mutationdblWRN-HumanWRNmutationdb(Warnerdisease)lWT1mutation-HumanWT1mutationdblX-ALDmutation-HumanABCD1mutati

32、ondb8、进化相关数据库及资源、进化相关数据库及资源lClustersofOrthologousGroups(COG)-Phylogeneticclassificationofproteinsfrom21completegenomeslXREFdb-Cross-referencingofmodelorganismgeneticswithmammalianphenotypeslTreeBASE-RelationaldbofphylogeneticinformationlTheTreeoflife-CollectionofWWWpagesonphylogenyandbiodiversityofo

33、rganismshttp:/phylogeny.arizona.edu/tree/8、专利数据库专利数据库lDPD-DNAPatentdblAgPatents-AgriculturalBiotechnologypatentsfromtheUSDA（农业生物技术专利）lUSPTOpatentdb-USAPatentandTrademark（商标）OfficepatentdblEspcenet-PatentinformationdatabasefromtheEuropeanPatentOffice(worldwidecoverage)lTheDelphionIntellectualProperty

34、Network(IPN)forsearching,viewing,andanalyzingpatentdocuments.9、资源目录服务器或网页资源目录服务器或网页lBioCatalog-TheBioCatalogatEBIlYellowBAGI-BioAccessGuidetotheInternetatHoustonUniversitylSoftwarelibraryfromGlDBCAT-DatabasescatalogatINFOBIOGENlMBDL-MolecularBiologyDatabaseListlAmosWWWlinkspagelNucleicAcidsResearchd

35、atabaseissueHuman（与人类基因有关的数据库）与人类基因有关的数据库）lCEPH-genotypedatabaselCEPHhomepage-aresearchlaboratorywhichconstructsmapsofthehumangenomelGeneMap99-AGeneMapoftheHumanGenome(NCBI)lOMIM-OnlineMendelianInheritanceinManlGENATLAS-HumangenesatlaslGeneClinics-MedicalgeneticsknowledgebaselGDB-Humangenesandgenomi

36、cmapslGeneCards-DbintegratinginformationonhumangenesHumanlUDB-UnifieddbforHumangenomemappinglEnsembl-HumangenomeannotationssitelUCSChumangenomeworkingdraftlTIGRHGI-TIGRHumanGeneIndexlHumanBACEndsDatabase-Non-redundanthumanBACendsequenceslHsUniGene-HumantranscriptsinGenBank(ESTclusters)lSTACK-Sequenc

37、eTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)HumanlAllgenes.org-Humanpredictedgeneindex/cataloglGenLink-HumangeneticsresourcelGENOTK-HumancDNAdblHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)lCGAP-CancerGenomeAnatomyProjectlSCDb-StemcelldbHumanlHuGeMap-Humangenomegenetic

38、andphysicalmapdatalG3-RH-StanfordG3andTNGradiationhybridmapslGB4-RH-Genebridge4(GB4)humanradiationhybridmapslRadiationHybridDatabase-RadiationhybridmapdataHumanchromosome18lChr1-Humanchromosome1atRockefellerUniversityMirroratEBIlChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenterlChr7-H

39、umanchromosome7dbatOntariosHospitalforSickChildrenlChr8SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome8Humanchromosome911lChr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9lChr9-Humanchromosome9dblChr10SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10lGTCChr10data-

40、Humanchromosome10datafromGenomeTherapeuticsCorporationlChr11SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome11l11DB-Humanchromosome11dbatImperialCollege(U.K.)Humanchromosome1216lChr12SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome12lChr13-Humanchromosome13dbatColumbialChr14SWISS

41、-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome14lChr15SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome15lChr15UBC-Humanchromosome15WWWpageatUBClChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16Humanchromosome1619lChr16LANL-Humanchromosome16dbatLosAlamosNationalLabora

42、torylChr16TIGR-Humanchromosome16dbatTIGRlChr17SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome17lChr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18lChr18-Humanchromosome18atBostonChildrensHospitallChr19SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19Humanchromoso

43、me2022lChr20SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome20lChr21SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21lChr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)lChr21atERI-Humanchromosome21genomicsequencedbfromtheEleanorRooseveltInstitutelChr22SWISS-PROTlist-LinkstoS

44、WISS-PROTentriesfromhumanchromosome22lChr22atSanger-SangerCenterchromosome22projectlChr22atHGC-Humangenomecenterforchromosome22HumanchromosomeXY（人类（人类XY染色体）染色体）lChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXlIXDB-IntegratedXchromosomedblChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfro

45、mhumanchromosomeYVertebrates（脊椎动物）lOMIA-OnlineMendelianInheritanceinAnimalslMGI-MouseGenomeInformatics(includes*Mouse GenomeDatabase(MGD)MirrorsinAustralia|UK|JapanlTIGRMGI-TIGRMouse*GeneIndexlMmUniGene-MousetranscriptsinGenBank(ESTclusters)lRatMAP-RatgenomedblTIGRRGI-TIGRRatGeneIndexlRnUnigene-Ratt

46、ranscriptsinGenBank(ESTclusters)(以上与老鼠有关的基因数据库）VertebrateslBovBASE-Bovinegenomedb(inUK)lBOVMAP-Bovinegenomedb(inFrance)（牛）lArk-Catcatgenomedb(猫）lHorseBASE-Horsegenomedb（马）lDGP-DogGenomeProject（狗）lPiGBASE-Piggenomedb（猪）lSheepBASE-Sheepgenomedb(alsoknownasSheepMap)MirrorinUK（羊）lMIS-MendelianInheritanc

47、einSheeplChickGBASE-Chickengenomedb（鸡）VertebrateslFugu-HGMPResourceCentreFuguProject(Fugurubripes)（河豚）lMedakafish-Mekadafish(Oryziaslatipes)serverlArk-Tilapia-Tilapia（罗非鱼）mossambicagenomedblThefishnet-Zebrafishserver（斑马鱼）lFishBase-GlobalinformationsystemonfishesMitochondrionandchloroplast（线立体和叶绿体）lG

48、OBASE-OrganelleGenomeDatabaselMitoDat-MendelianInheritanceandtheMitochondriondb(mitochondrialnucleargenes)lMITOMAP-HumanmitochondrialgenomedblMmtDB-MetazoamitochondrialDNAvariantsdb（后生动物）lMitBASE-IntegratedmitochondrialDNAdblMitBASE-Pilot-DbofS.cerevisiaenucleargenesinvolvedinmitochondrialbiogenesis

49、lHvrBase-PrimatesmtDNAcontrolregionsequencescompilationMitochondrionandchloroplastlMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)lMITOP-Mitochondrialproteins,genesanddiseaseslAMmtDB-MetazoanmitochondrialDNAsequencesInsects（昆虫）（昆虫）lDrosophilaSWISS-PROTlist-LinkstoDrosophilaSWISS-PR

50、OTentries（果蝇）lFlyBase-DrosophilageneticandmoleculardbMirroratEBIlFlyView-DrosophilaimagedblGIFTS-GeneInteractionsintheFlyTrans-WorldServerlFlyNets-DbofmolecularinteractionsinDrosophilamelanogasterlSOS-DGBD-DbofDrosophilaDNAsequencesannotatedwithregulatorybindingsiteslMosquitoGenomics（蚊子）Invertebrate