很好—生物信息相关数据库资源介绍课件.ppt

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1、生物信息学生物信息学数据库资源大全数据库资源大全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

2、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）、核酸序列数据库lBIOSINO我国的核酸序列公共数据库lEMBL-EMBLNucleotidesequencedatabase(EBI)lGenBank-GenBank

3、NucleotideSequencedatabase(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)-AcatalogueofusefulWebsitesforGenomicswithasetofcollectionsofgenomedatabaseslGSDB-GenomeSequenceda

4、tabase(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-AncientconserveduntranslatedDNAsequencesdblCodonUsageDb-Thefrequencyofcodonuseineachorganismismadesearchabl

5、ethroughthisWorldWideWebsite.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-RibosomaldbProjectlgRNAsdb-GuideRNAdblPLACE-Plantcis-actingregulatoryDNAelementsdb5）其它）其它

6、核酸数据库lPlantCARE-Plantcis-actingregulatoryDNAelementsdblsRNAdb-SmallRNAdblssurRNA-SmallribosomalsubunitdbllsurRNA-Largeribosomalsubunitdbl5SrRNA-5SribosomalRNAdbltmRNAWebsiteltmRDB-tmRNAdBltRNA-tRNAcompilation（编辑）（编辑）fromtheUniversityofBayreuthluRNADB-uRNAdb5）其他）其他核酸数据库lRNAediting-RNAeditingsitelRNAm

7、oddb-RNAmodificationdblTelDB-MultimediaTelomere（端粒）ResourcelTRADAT-TRAnscriptionDatabasesandAnalysisToolslSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)（类病毒）5）Transgenics（转基因）lCreTransgenicDatabase-CretransgenicmouselineslTransgenic/TargetedMutationDatabase-Informationontransgenicanimalsand

8、targetedmutations2.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创建蛋白质专家分析系统ExPASy，北京)lMIPS(Munichinformationcenterforproteinsequence)

9、（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(Automaticallygenerated)lPfam-Proteinfamiliesdb(HMMderived)MirroratSangerlPRINTS-ProteinMotiffingerpri

10、ntdblProDom-Proteindomaindb(Automaticallygenerated)lPROTOMAP-Anautomatichierarchical（分等级）（分等级）classificationofSWISS-PROTproteinslSBASE-SBASEdomaindb(Proteindomainsequencelibrary)lSMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)lProClass-Proteinsequencealig

11、nmentsandcurationofproteinfamilies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-Dbofcomparativeproteinstructuremodel

12、slCATH-UCLBSMstructuralclassificationofproteinslSCOP-StructuralclassificationofproteinsMirroratUSA|Israel|Singapore|AustralialMol_R_Us-MoleculesRUs,browserforPDBlBMMDomainServer-BiomolecularModellingLaboratory(ICRF)proteindomainserverlPRESAGE-Collaborativeresourceforstructuralgenomics蛋白质三维结构和相关数据库蛋白

13、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蛋白质二维凝

14、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-ProteininteractiondblProNet-Protein-ProteininteractiondblCANSITE-SignalTransductions（信号传导）（信号传导）Webl

15、SPAD-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（醛脱氢酶，l醛氧化酶）genesuperfamilydblAminoacyl-tRNAsynthetasesinSWISS-PROT-Listofaminoacyl

16、-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）lAntibodyresourcepage-LinkstoantibodyrelatedWebresources（抗体）lAustralianvenomandtoxindb（澳大利亚蛇毒）lBacil

17、lusthuringiensistoxinspecificitydb（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-handCaBP-EF-handcalcium-bindingproteinsdblCAZy-Carbohydrate-ActiveenZYmesWebsitelCBSdom

18、ainCystathionine（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-DatabaseoninformationaboutCDantigenslChaperonin-InformationonGroELandGroESchaperoninslConotoxins-Informationonconotoxinsfroma

19、Websiteonconeshellsl。etc。4、糖类相关数据库、糖类相关数据库lCarbBank-ComplexCarbohydrateStructureDatabaselGlycoSuiteDB-DbofglycanstructureslTGN-TheGlycoscienceNetworklFCCA-ForumCarbohydratesComingofAgelCARBHYD-CarbohydrateinformationWWWsiteslMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides（单糖）5、蛋

20、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-Proteinproductsandexpressionpatternsofalternatively-splicedgeneslAxeldb-GeneexpressioninXenopuslBodyMap-Humanandmousegeneexpressio

21、ndatalEpoDB-GenesexpressedinvertebrateRBClFlyView-Drosophiladevelopmentandgenetics（果蝇）lGeneExpressionDatabase(GXD)-Mousegeneexpressionandgenomics（鼠）lKidneyDevelopmentDatabaseKidney（肾）developmentandgeneexpression6、基因表达数据库、基因表达数据库lMAGEST-Ascidian(Halocynthiaroretzi)geneexpressionpatternslMouseAtlasand

22、GeneExpressionDatabase-Spatially-mappedgeneexpressiondatalPEDB-Normalandaberrantprostate（正常、异常前列腺）geneexpressionlToothDevelopmentDatabase-GeneexpressionindentaltissuelTRIPLES-TRansposon-InsertionPhenotypes,LocalizationandExpressioninSaccharomyces（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-HumanGeneMuta

23、tiondblSVD-SequencevariationdblHGBASE-HumanGenicBi-AllelicSequencesdblTheSNPconsortiumldbSNP-Humansinglenucleotidepolymorphism(SNP)db（单核苷酸多态性数据库）lListofmutationdatabasesfromOMIMlListofmutationdatabasesfromIMT(Finland)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

24、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)7、人类基因突

25、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-Dreifu

26、ssmusculardystrophy)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lFBN1mutation-Humanfibrillin1mutationdb(Marfansyndrome)lG6PD-HumanG6PDdeficiencyre

27、sourcelGaltmutation-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-2receptorgamma)mutationdb(X-SCID)lL1CAMmutation-HumanL1CAMmutationdblLDLRmutation-HumanLDLRmu

28、tationdb(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-NeuronalCeroidLipofuscinosesmutationdblOTCase-Humanornithinetranscarbamylase(OTCase)websitelCytochromeP450allelesnomen

29、claturelp53mutationdb-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-HumanPAX6mutationdblPrion-PrionandpriondiseasewebsitelRAG1base-HumanRAG1mutationdblRAG2bas

30、e-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及疾病相关数据库lTSC-TSC(TSC1/TSC2)variationdblTSC2-Cardiff-RotterdamTuberousSclerosis(T

31、S)db(Tuberin;TSC2)lTGDB-TumorgenedblVMD2mutation-HumanVMD2mutationdblvWFmutation-HumanvonWillebrandfactor(vWF)mutationdblWRN-HumanWRNmutationdb(Warnerdisease)lWT1mutation-HumanWT1mutationdblX-ALDmutation-HumanABCD1mutationdb8、进化相关数据库及资源、进化相关数据库及资源lClustersofOrthologousGroups(COG)-Phylogeneticclassif

32、icationofproteinsfrom21completegenomeslXREFdb-Cross-referencingofmodelorganismgeneticswithmammalianphenotypeslTreeBASE-RelationaldbofphylogeneticinformationlTheTreeoflife-CollectionofWWWpagesonphylogenyandbiodiversityoforganismshttp:/phylogeny.arizona.edu/tree/8、专利数据库专利数据库lDPD-DNAPatentdblAgPatents-

33、AgriculturalBiotechnologypatentsfromtheUSDA（农业生物技术专利）lUSPTOpatentdb-USAPatentandTrademark（商标）OfficepatentdblEspcenet-PatentinformationdatabasefromtheEuropeanPatentOffice(worldwidecoverage)lTheDelphionIntellectualPropertyNetwork(IPN)forsearching,viewing,andanalyzingpatentdocuments.9、资源目录服务器或网页资源目录服务器

34、或网页lBioCatalog-TheBioCatalogatEBIlYellowBAGI-BioAccessGuidetotheInternetatHoustonUniversitylSoftwarelibraryfromGlDBCAT-DatabasescatalogatINFOBIOGENlMBDL-MolecularBiologyDatabaseListlAmosWWWlinkspagelNucleicAcidsResearchdatabaseissueHuman（与人类基因有关的数据库）与人类基因有关的数据库）lCEPH-genotypedatabaselCEPHhomepage-ar

35、esearchlaboratorywhichconstructsmapsofthehumangenomelGeneMap99-AGeneMapoftheHumanGenome(NCBI)lOMIM-OnlineMendelianInheritanceinManlGENATLAS-HumangenesatlaslGeneClinics-MedicalgeneticsknowledgebaselGDB-HumangenesandgenomicmapslGeneCards-DbintegratinginformationonhumangenesHumanlUDB-UnifieddbforHumang

36、enomemappinglEnsembl-HumangenomeannotationssitelUCSChumangenomeworkingdraftlTIGRHGI-TIGRHumanGeneIndexlHumanBACEndsDatabase-Non-redundanthumanBACendsequenceslHsUniGene-HumantranscriptsinGenBank(ESTclusters)lSTACK-SequenceTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)HumanlAllgenes.org

37、-Humanpredictedgeneindex/cataloglGenLink-HumangeneticsresourcelGENOTK-HumancDNAdblHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)lCGAP-CancerGenomeAnatomyProjectlSCDb-StemcelldbHumanlHuGeMap-HumangenomegeneticandphysicalmapdatalG3-RH-StanfordG3andTNGradiationhybridmapslGB4-RH-Genebridge4(

38、GB4)humanradiationhybridmapslRadiationHybridDatabase-RadiationhybridmapdataHumanchromosome18lChr1-Humanchromosome1atRockefellerUniversityMirroratEBIlChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenterlChr7-Humanchromosome7dbatOntariosHospitalforSickChildrenlChr8SWISS-PROTlist-LinkstoSWI

39、SS-PROTentriesfromhumanchromosome8Humanchromosome911lChr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9lChr9-Humanchromosome9dblChr10SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10lGTCChr10data-Humanchromosome10datafromGenomeTherapeuticsCorporationlChr11SWISS-PROTlist-Links

40、toSWISS-PROTentriesfromhumanchromosome11l11DB-Humanchromosome11dbatImperialCollege(U.K.)Humanchromosome1216lChr12SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome12lChr13-Humanchromosome13dbatColumbialChr14SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome14lChr15SWISS-PROTlist-Link

41、stoSWISS-PROTentriesfromhumanchromosome15lChr15UBC-Humanchromosome15WWWpageatUBClChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16Humanchromosome1619lChr16LANL-Humanchromosome16dbatLosAlamosNationalLaboratorylChr16TIGR-Humanchromosome16dbatTIGRlChr17SWISS-PROTlist-LinkstoSWISS-PROTen

42、triesfromhumanchromosome17lChr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18lChr18-Humanchromosome18atBostonChildrensHospitallChr19SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19Humanchromosome2022lChr20SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome20lChr21SW

43、ISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21lChr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)lChr21atERI-Humanchromosome21genomicsequencedbfromtheEleanorRooseveltInstitutelChr22SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome22lChr22atSanger-SangerCenterchromosome22proj

44、ectlChr22atHGC-Humangenomecenterforchromosome22HumanchromosomeXY（人类（人类XY染色体）染色体）lChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXlIXDB-IntegratedXchromosomedblChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeYVertebrates（脊椎动物）lOMIA-OnlineMendelianInheritanceinAnimalslMGI-

45、MouseGenomeInformatics(includes*Mouse GenomeDatabase(MGD)MirrorsinAustralia|UK|JapanlTIGRMGI-TIGRMouse*GeneIndexlMmUniGene-MousetranscriptsinGenBank(ESTclusters)lRatMAP-RatgenomedblTIGRRGI-TIGRRatGeneIndexlRnUnigene-RattranscriptsinGenBank(ESTclusters)(以上与老鼠有关的基因数据库）VertebrateslBovBASE-Bovinegenomed

46、b(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）VertebrateslFugu-HGMPResourceCentreFuguPro

47、ject(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）lGOBASE-OrganelleGenomeDatabaselMitoDat-MendelianInheritanceandtheMitochondriondb(

48、mitochondrialnucleargenes)lMITOMAP-HumanmitochondrialgenomedblMmtDB-MetazoamitochondrialDNAvariantsdb（后生动物）lMitBASE-IntegratedmitochondrialDNAdblMitBASE-Pilot-DbofS.cerevisiaenucleargenesinvolvedinmitochondrialbiogenesislHvrBase-PrimatesmtDNAcontrolregionsequencescompilationMitochondrionandchloropla

49、stlMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)lMITOP-Mitochondrialproteins,genesanddiseaseslAMmtDB-MetazoanmitochondrialDNAsequencesInsects（昆虫）（昆虫）lDrosophilaSWISS-PROTlist-LinkstoDrosophilaSWISS-PROTentries（果蝇）lFlyBase-DrosophilageneticandmoleculardbMirroratEBIlFlyView-Drosoph

50、ilaimagedblGIFTS-GeneInteractionsintheFlyTrans-WorldServerlFlyNets-DbofmolecularinteractionsinDrosophilamelanogasterlSOS-DGBD-DbofDrosophilaDNAsequencesannotatedwithregulatorybindingsiteslMosquitoGenomics（蚊子）Invertebrates（无脊柱动物（无脊柱动物lWormBase-C.elegansdbMirroratSangerlC.elegansWWWserver-atUniversity