生物信息学相关数据库资源介绍市公开课一等奖百校联赛特等奖课件.pptx

生物信息学生物信息学相关数据库资源介绍相关数据库资源介绍刘吉平Reference：www.biosino.org第1页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、其它）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.基因表示数据库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、其它）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.基因表示数据库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第2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）、核酸序列数据库lBIOSINO我国核酸序列公共数据库lEMBL-EMBLNucleotidesequencedatabase(EBI)lGenBank-GenBankNucleotideSequencedatabase(NCBI)lDDBJ-DNADataBankofJapanldbEST-DatabaseofExpressedSequenceTags（表示序列标签）(NCBI)ldbSTS-DatabaseofSequenceTaggedSites（序列标签位点）(NCBI)第3页2）.基因组及相关数据库GenomicDatabaseslGenomeWeb(HGMP)-AcatalogueofusefulWebsitesforGenomicswithasetofcollectionsofgenomedatabaseslGSDB-GenomeSequencedatabase(NCGR)lGOLD-GenomesOn-linedbl一些数据库直接链接第4页3）.核酸三维结构数据库lNDB-NucleicAcidDatabank(3Dstructures)lBNASDB-NucleicacidstructuredbfromUniversityofPune第5页4）.其它lAsDb-AberrantSplicingdb（异常拼接）（异常拼接）lACUTS-AncientconserveduntranslatedDNAsequencesdblCodonUsageDb-ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.lEPD-EukaryoticPromoterdb（真核开启子）（真核开启子）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-RibosomaldbProjectlgRNAsdb-GuideRNAdblPLACE-Plantcis-actingregulatoryDNAelementsdb第6页5）其它）其它核酸数据库lPlantCARE-Plantcis-actingregulatoryDNAelementsdblsRNAdb-SmallRNAdblssurRNA-SmallribosomalsubunitdbllsurRNA-Largeribosomalsubunitdbl5SrRNA-5SribosomalRNAdbltmRNAWebsiteltmRDB-tmRNAdBltRNA-tRNAcompilation（编辑）（编辑）fromtheUniversityofBayreuthluRNADB-uRNAdb第7页5）其它）其它核酸数据库lRNAediting-RNAeditingsitelRNAmoddb-RNAmodificationdblTelDB-MultimediaTelomere（端粒）ResourcelTRADAT-TRAnscriptionDatabasesandAnalysisToolslSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)（类病毒）第8页5）Transgenics（转基因）lCreTransgenicDatabase-CretransgenicmouselineslTransgenic/TargetedMutationDatabase-Informationontransgenicanimalsandtargetedmutations第9页2.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(SIB+EBI,EBI创建蛋白质教授分析系统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）第10页蛋白质相关数据库蛋白质相关数据库lPROSITE-PROSITEdictionaryofproteinsitesandpatternslInterPro-IntegratedResourcesofProteinsDomainsandFunctionalSiteslBLOCKS-BLOCKSdblDOMO-Proteindomaindb(Automaticallygenerated)lPfam-Proteinfamiliesdb(HMMderived)MirroratSangerlPRINTS-ProteinMotiffingerprintdblProDom-Proteindomaindb(Automaticallygenerated)lPROTOMAP-Anautomatichierarchical（分等级）（分等级）classificationofSWISS-PROTproteinslSBASE-SBASEdomaindb(Proteindomainsequencelibrary)lSMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)lProClass-Proteinsequencealignmentsandcurationofproteinfamilies第11页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-AutomaticallygeneratedproteinmodelsdblModBase-DbofcomparativeproteinstructuremodelslCATH-UCLBSMstructuralclassificationofproteinslSCOP-StructuralclassificationofproteinsMirroratUSA|Israel|Singapore|AustralialMol_R_Us-MoleculesRUs,browserforPDBlBMMDomainServer-BiomolecularModellingLaboratory(ICRF)proteindomainserverlPRESAGE-Collaborativeresourceforstructuralgenomics第12页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-ProteinsequencealignmentsandcurationofproteinfamilieslKabat-KabatdbofproteinofimmunologicalinterestlPMD-ProteinMutantdb第13页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-Phoretixpageoflinksto2Dgeldb第14页3、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-ProteininteractiondblProNet-Protein-ProteininteractiondblCANSITE-SignalTransductions（信号传导）（信号传导）WeblSPAD-SignalingpathwaydblCSNDB-CellSignalingNetworksdb第15页DNA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第16页特定基因或蛋白质数据库特定基因或蛋白质数据库lAAA-AAAfamilyofATPasesserverAcetylcholinesteraseslALDH-Aldehydedehydrogenase（醛脱氢酶，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第17页特定基因或蛋白质数据库特定基因或蛋白质数据库lAMSDb-Antimicrobialsequencesdb（抗菌）lAntibodyresourcepage-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第18页特定基因或蛋白质数据库特定基因或蛋白质数据库lEF-handCaBP-EF-handcalcium-bindingproteinsdblCAZy-Carbohydrate-ActiveenZYmesWebsitelCBSdomainCystathionine（胱硫醚,丙氨酸丁氨酸硫醚）BetaSynthasedomainWWWpagelCDantigensinSWISS-PROT-Nomenclatureforsurfaceproteinsofhumanleucocytes(白血球CD)第19页特定基因或蛋白质数据库特定基因或蛋白质数据库lCDantigensinPROW-DatabaseoninformationaboutCDantigenslChaperonin-InformationonGroELandGroESchaperoninslConotoxins-InformationonconotoxinsfromaWebsiteonconeshellsl。etc。第20页4、糖类相关数据库、糖类相关数据库lCarbBank-ComplexCarbohydrateStructureDatabaselGlycoSuiteDB-DbofglycanstructureslTGN-TheGlycoscienceNetworklFCCA-ForumCarbohydratesComingofAgelCARBHYD-CarbohydrateinformationWWWsiteslMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides（单糖）第21页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-DbofAminoAcidModifications第22页6、基因表示数据库基因表示数据库lASDB-Proteinproductsandexpressionpatternsofalternatively-splicedgeneslAxeldb-GeneexpressioninXenopuslBodyMap-HumanandmousegeneexpressiondatalEpoDB-GenesexpressedinvertebrateRBClFlyView-Drosophiladevelopmentandgenetics（果蝇）lGeneExpressionDatabase(GXD)-Mousegeneexpressionandgenomics（鼠）lKidneyDevelopmentDatabaseKidney（肾）developmentandgeneexpression第23页6、基因表示数据库、基因表示数据库lMAGEST-Ascidian(Halocynthiaroretzi)geneexpressionpatternslMouseAtlasandGeneExpressionDatabase-Spatially-mappedgeneexpressiondatalPEDB-Normalandaberrantprostate（正常、异常前列腺）geneexpressionlToothDevelopmentDatabase-GeneexpressionindentaltissuelTRIPLES-TRansposon-InsertionPhenotypes,LocalizationandExpressioninSaccharomyces（酵母）第24页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)第25页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-Dbofmutationscausingtetrahydrobiopterindeficiencies（缺乏四氢生物蝶呤缺乏四氢生物蝶呤lBLMbase-HumanBLMmutationdb(Bloomsnydrom)第26页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(CFTR)（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第27页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lFBN1mutation-Humanfibrillin1mutationdb(Marfansyndrome)lG6PD-HumanG6PDdeficiencyresourcelGaltmutation-Humangalactose-1-phosphateuridylyltransferasemutationdb(Galactosemia)第28页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-2receptorgamma)mutationdb(X-SCID)lL1CAMmutation-HumanL1CAMmutationdblLDLRmutation-HumanLDLRmutationdb(Familialhypercholesterolemia)lLQTSdb-LongQTsyndromedblNCF1base-HumanNCF1mutationdblNCF2base-HumanNCF2mutationdb第29页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-NeuronalCeroidLipofuscinosesmutationdblOTCase-Humanornithinetranscarbamylase(OTCase)websitelCytochromeP450allelesnomenclaturelp53mutationdb-UniversityofTokyop53mutationdblGermlinep53mutationdb-UniversityofPraguedbofgermlinep53mutationslPAHdb-Humanphenylalaninehydroxylase(PAH)mutationdb第30页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-HumanPAX6mutationdblPrion-PrionandpriondiseasewebsitelRAG1base-HumanRAG1mutationdblRAG2base-HumanRAG2mutationdblRB1base-Humanretinoblastoma-associatedprotein(RB)mutationdblRetNet-RetinalInformationNetworklRetinaInternationalScientificNewsletter-InformationonRetinalgenes,proteinsanddiseases第31页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lTSC-TSC(TSC1/TSC2)variationdblTSC2-Cardiff-RotterdamTuberousSclerosis(TS)db(Tuberin;TSC2)lTGDB-TumorgenedblVMD2mutation-HumanVMD2mutationdblvWFmutation-HumanvonWillebrandfactor(vWF)mutationdblWRN-HumanWRNmutationdb(Warnerdisease)lWT1mutation-HumanWT1mutationdblX-ALDmutation-HumanABCD1mutationdb第32页8、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-CollectionofWWWpagesonphylogenyandbiodiversityoforganismshttp:/phylogeny.arizona.edu/tree/第33页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)lTheDelphionIntellectualPropertyNetwork(IPN)forsearching,viewing,andanalyzingpatentdocuments.第34页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-MolecularBiologyDatabaseListlAmosWWWlinkspagelNucleicAcidsResearchdatabaseissue第35页Human（与人类基因相关数据库）与人类基因相关数据库）lCEPH-genotypedatabaselCEPHhomepage-aresearchlaboratorywhichconstructsmapsofthehumangenomelGeneMap99-AGeneMapoftheHumanGenome(NCBI)lOMIM-OnlineMendelianInheritanceinManlGENATLAS-HumangenesatlaslGeneClinics-MedicalgeneticsknowledgebaselGDB-HumangenesandgenomicmapslGeneCards-Dbintegratinginformationonhumangenes第36页HumanlUDB-UnifieddbforHumangenomemappinglEnsembl-HumangenomeannotationssitelUCSChumangenomeworkingdraftlTIGRHGI-TIGRHumanGeneIndexlHumanBACEndsDatabase-Non-redundanthumanBACendsequenceslHsUniGene-HumantranscriptsinGenBank(ESTclusters)lSTACK-SequenceTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)第37页HumanlAllgenes.org-Humanpredictedgeneindex/cataloglGenLink-HumangeneticsresourcelGENOTK-HumancDNAdblHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)lCGAP-CancerGenomeAnatomyProjectlSCDb-Stemcelldb第38页HumanlHuGeMap-HumangenomegeneticandphysicalmapdatalG3-RH-StanfordG3andTNGradiationhybridmapslGB4-RH-Genebridge4(GB4)humanradiationhybridmapslRadiationHybridDatabase-Radiationhybridmapdata第39页Humanchromosome18lChr1-Humanchromosome1atRockefellerUniversityMirroratEBIlChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenterlChr7-Humanchromosome7dbatOntariosHospitalforSickChildrenlChr8SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome8第40页Humanchromosome911lChr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9lChr9-Humanchromosome9dblChr10SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10lGTCChr10data-Humanchromosome10datafromGenomeTherapeuticsCorporationlChr11SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome11l11DB-Humanchromosome11dbatImperialCollege(U.K.)第41页Humanchromosome1216lChr12SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome12lChr13-Humanchromosome13dbatColumbialChr14SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome14lChr15SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome15lChr15UBC-Humanchromosome15WWWpageatUBClChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16第42页Humanchromosome1619lChr16LANL-Humanchromosome16dbatLosAlamosNationalLaboratorylChr16TIGR-Humanchromosome16dbatTIGRlChr17SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome17lChr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18lChr18-Humanchromosome18atBostonChildrensHospitallChr19SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19第43页Humanchromosome2022lChr20SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome20lChr21SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21lChr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)lChr21atERI-Humanchromosome21genomicsequencedbfromtheEleanorRooseveltInstitutelChr22SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome22lChr22atSanger-SangerCenterchromosome22projectlChr22atHGC-Humangenomecenterforchromosome22第44页HumanchromosomeXY（人类（人类XY染色体）染色体）lChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXlIXDB-IntegratedXchromosomedblChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeY第45页Vertebrates（脊椎动物）lOMIA-OnlineMendelianInheritanceinAnimalslMGI-MouseGenomeInformatics(includes*Mouse GenomeDatabase(MGD)MirrorsinAustralia|UK|JapanlTIGRMGI-TIGRMouse*GeneIndexlMmUniGene-MousetranscriptsinGenBank(ESTclusters)lRatMAP-RatgenomedblTIGRRGI-TIGRRatGeneIndexlRnUnigene-RattranscriptsinGenBank(ESTclusters)(以上与老鼠相关基因数据库）第46页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-MendelianInheritanceinSheeplChickGBASE-Chickengenomedb（鸡）第47页VertebrateslFugu-HGMPResourceCentreFuguProject(Fugurubripes)（河豚）lMedakafish-Mekadafish(Oryziaslatipes)serverlArk-Tilapia-Tilapia（罗非鱼）mossambicagenomedblThefishnet-Zebrafishserver（斑马鱼）lFishBase-Globalinformationsystemonfishes第48页Mitochondrionandchloroplast（线立体和叶绿体）lGOBASE-OrganelleGenomeDatabaselMitoDat-MendelianInheritanceandtheMitochondriondb(mitochondrialnucleargenes)lMITOMAP-HumanmitochondrialgenomedblMmtDB-MetazoamitochondrialDNAvariantsdb（后生动物）lMitBASE-IntegratedmitochondrialDNAdblMitBASE-Pilot-DbofS.cerevisiaenucleargenesinvolvedinmitochondrialbiogenesislHvrBase-PrimatesmtDNAcontrolregionsequencescompilation第49页MitochondrionandchloroplastlMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)lMITOP-Mitochondrialproteins,genesanddiseaseslAMmtDB-MetazoanmitochondrialDNAsequences第50页Insects（昆虫）（昆虫）lDrosophilaSWISS-PROTlist-LinkstoDrosophilaSWISS-PROTentries（果蝇）lFlyBase-DrosophilageneticandmoleculardbMirroratEBIlFlyView-DrosophilaimagedblGIFTS-GeneInteractionsintheFlyTrans-WorldServerlFlyNets-Dbofmolecularinteractio