生物信息学相关数据库资源介绍省公共课一等奖全国赛课获奖课件.pptx

核酸及其相关数据库（核酸序列、基因组相关数核酸及其相关数据库（核酸序列、基因组相关数据库、核酸三维结构、其它）据库、核酸三维结构、其它）2.蛋白质相关数据库蛋白质相关数据库（蛋白质序列、蛋白质三维结构、蛋（蛋白质序列、蛋白质三维结构、蛋白质组（二维凝胶电泳数据库）、信号传导及蛋白质白质组（二维凝胶电泳数据库）、信号传导及蛋白质-蛋白蛋白质相互作用相关数据库、质相互作用相关数据库、DNA和蛋白质相互作用数据库）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基因或蛋白质一些特定数据库4.糖类及其相关数据库糖类及其相关数据库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6.基因表示数据库基因表示数据库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8.进化相关数据库及资源专利数据库进化相关数据库及资源专利数据库资源目录服务器或网页第2页一、核酸及其相关数据库一、核酸及其相关数据库1、核酸序列数据库、核酸序列数据库nEMBL-EMBLNucleotidesequencedatabase(EBI)*nGenBank-GenBankNucleotideSequencedatabase(NCBI)*nDDBJ-DNADataBankofJapan*nBIOSINO我国核酸序列公共数据库ndbEST-DatabaseofExpressedSequenceTags(NCBI)ndbSTS-DatabaseofSequenceTaggedSites(NCBI)第3页2.基因组及相关数据库GenomicDatabasesnGenomeWeb(HGMP)-AcatalogueofusefulWebsitesforGenomicswithasetofcollectionsofgenomedatabasesnGSDB-GenomeSequencedatabase(NCGR)nGOLD-GenomesOn-linedbn一些数据库直接链接第4页3.核酸三维结构数据库nNDB-NucleicAcidDatabank(3Dstructures)nBNASDB-NucleicacidstructuredbfromUniversityofPune第5页4.其它nAsDb-AberrantSplicingdbnACUTS-AncientconserveduntranslatedDNAsequencesdbnCodonUsageDb-ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.nEPD-EukaryoticPromoterdbnHOVERGEN-HomologousVertebrateGenesdbnIMGT-ImMunoGeneTicsdbMirroratEBInISIS-IntronSequenceandInformationSystemnRDP-RibosomaldbProjectngRNAsdb-GuideRNAdbnPLACE-Plantcis-actingregulatoryDNAelementsdb第6页其它其它nPlantCARE-Plantcis-actingregulatoryDNAelementsdbnsRNAdb-SmallRNAdbnssurRNA-SmallribosomalsubunitdbnlsurRNA-Largeribosomalsubunitdbn5SrRNA-5SribosomalRNAdbntmRNAWebsitentmRDB-tmRNAdBntRNA-tRNAcompilationfromtheUniversityofBayreuthnuRNADB-uRNAdb第7页其它其它nRNAediting-RNAeditingsitenRNAmoddb-RNAmodificationdbnTelDB-MultimediaTelomereResourcenTRADAT-TRAnscriptionDatabasesandAnalysisToolsnSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)第8页TransgenicsnCreTransgenicDatabase-CretransgenicmouselinesnTransgenic/TargetedMutationDatabase-Informationontransgenicanimalsandtargetedmutations第9页二.蛋白质序列和相关数据库nSWISS-PROT-SWISS-PROTannotatedproteinsequencedbnPIR-international-TheProteinInformationResource(proteinsequence)nMIPS-Martinsriedinstituteforproteinsequenceandhomologydataandyeastgenomeinformation第10页蛋白质及其相关数据库蛋白质及其相关数据库nPROSITE-PROSITEdictionaryofproteinsitesandpatternsnInterPro-IntegratedResourcesofProteinsDomainsandFunctionalSitesnBLOCKS-BLOCKSdbnDOMO-Proteindomaindb(Automaticallygenerated)nPfam-Proteinfamiliesdb(HMMderived)MirroratSangernPRINTS-ProteinMotiffingerprintdbnProDom-Proteindomaindb(Automaticallygenerated)nPROTOMAP-AnautomatichierarchicalclassificationofSWISS-PROTproteinsnSBASE-SBASEdomaindb(Proteindomainsequencelibrary)nSMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)nProClass-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nPDB-ProteinDataBankMirrorsinEBInBioMagResBank-Repositoryfordataonproteins,peptides,andnucleicacidsfromNMRspectroscopynSWISS-MODELRepository-AutomaticallygeneratedproteinmodelsdbnModBase-DbofcomparativeproteinstructuremodelsnCATH-UCLBSMstructuralclassificationofproteinsnSCOP-StructuralclassificationofproteinsMirroratUSA|Israel|Singapore|AustralianMol_R_Us-MoleculesRUs,browserforPDBnBMMDomainServer-BiomolecularModellingLaboratory(ICRF)proteindomainservernPRESAGE-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nSBASE-SBASEdomaindb(Proteindomainsequencelibrary)nSMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)nProClass-ProteinsequencealignmentsandcurationofproteinfamiliesnKabat-KabatdbofproteinofimmunologicalinterestnPMD-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nWORLD-2DPAGE-Acompleteindexof2D-PAGEdbandserversnPhoretixlinks-Phoretixpageoflinksto2Dgeldb第14页三、信号传导及蛋白质三、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nDIP-DbofInteractingProteinsnINTERACT-Protein-ProteininteractiondbnProNet-Protein-ProteininteractiondbnCANSITE-SignalTransductionsWebnSPAD-SignalingpathwaydbnCSNDB-CellSignalingNetworksdb第15页四、四、DNA和蛋白质相互作用数据库和蛋白质相互作用数据库nDPInteract-DNA-Proteinsinteractionsdb第16页五、特定基因或蛋白质数据库五、特定基因或蛋白质数据库nAAA-AAAfamilyofATPasesserverAcetylcholinesterasesnALDH-AldehydedehydrogenasegenesuperfamilydbnAminoacyl-tRNAsynthetasesinSWISS-PROT-Listofaminoacyl-tRNAsynthetasesinSWISS-PROTnAARSDB-Aminoacyl-tRNAsynthetasesdbnAllergensinSWISS-PROT-NomenclatureandindexofallergensinSWISS-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nAMSDb-AntimicrobialsequencesdbnAntibodyresourcepage-LinkstoantibodyrelatedWebresourcesnAustralianvenomandtoxindbnBacillusthuringiensistoxinspecificitydbnTFII-BasaltranscriptionfactorsnBloodgroupantigensinSWISS-PROTnBCGD-BreastcancergenesdbfromMBCRnBRENDA-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nEF-handCaBP-EF-handcalcium-bindingproteinsdbnCAZy-Carbohydrate-ActiveenZYmesWebsitenCBSdomain-CystathionineBetaSynthasedomainWWWpagenCDantigensinSWISS-PROT-Nomenclatureforsurfaceproteinsofhumanleucocytes(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nCDantigensinPROW-DatabaseoninformationaboutCDantigensnChaperonin-InformationonGroELandGroESchaperoninsnConotoxins-InformationonconotoxinsfromaWebsiteonconeshells。etc。第20页糖类相关数据库糖类相关数据库nCarbBank-ComplexCarbohydrateStructureDatabaseGlycoSuiteDB-DbofglycanstructuresnTGN-TheGlycoscienceNetworknFCCA-ForumCarbohydratesComingofAgenCARBHYD-CarbohydrateinformationWWWsitesnMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides第21页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nO-GlycBase-O-glycosylatedproteinsdbnPhosphoBase-PhosphorylationsitesdbnRESID-DbofAminoAcidModifications第22页基因表示数据库基因表示数据库nASDB-Proteinproductsandexpressionpatternsofalternatively-splicedgenesnAxeldb-GeneexpressioninXenopusnBodyMap-HumanandmousegeneexpressiondatanEpoDB-GenesexpressedinvertebrateRBCnFlyView-DrosophiladevelopmentandgeneticsnGeneExpressionDatabase(GXD)-MousegeneexpressionandgenomicsnKidneyDevelopmentDatabase-Kidneydevelopmentandgeneexpression第23页基因表示数据库基因表示数据库nMAGEST-Ascidian(Halocynthiaroretzi)geneexpressionpatternsnMouseAtlasandGeneExpressionDatabase-Spatially-mappedgeneexpressiondatanPEDB-NormalandaberrantprostategeneexpressionnToothDevelopmentDatabase-GeneexpressionindentaltissuenTRIPLES-TRansposon-InsertionPhenotypes,LocalizationandExpressioninSaccharomyces第24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nHMGD-HumanGeneMutationdbSVD-SequencevariationdbnHGBASE-HumanGenicBi-AllelicSequencesdbnTheSNPconsortiumndbSNP-Humansinglenucleotidepolymorphism(SNP)dbnListofmutationdatabasesfromOMIMListofmutationdatabasesfromIMT(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nADB-Albinismdb(Mutationsinhumangenescausingalbinism)Alpha-glucosidase-Informationabouthumanacidalpha-glucosidase(GSD-II)nARmutations-HumanandrogenreceptormutationdbnAntithrombinmutationdbnAsthmaandAllergygenedbnBIOMDB-DbofmutationscausingtetrahydrobiopterindeficienciesnBLMbase-HumanBLMmutationdb(Bloomsnydrom)第26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nBTKbase-HumanBTKmutationdb(X-linkedagammaglobulinemia)nCD40Lbase-HumanCD40ligandmutationdbnCOL1/3mutation-HumanTypeIandIIIcollagenmutationdbnCFTRmutation-Humancysticfibrosismutationdb(CFTR)nEMDdb-HumanEmerin(EMD)mutationdb(Emery-Dreifussmusculardystrophy)nKMeyeDB-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nFVIImutation-HumanFactorVIImutationdbnHAMSTeRS-HumanFactorVIIImutationdb(HaemophiliaA)nHAeMB-HumanFactorIXmutationdb(HaemophiliaB)nFBN1mutation-Humanfibrillin1mutationdb(Marfansyndrome)nG6PD-HumanG6PDdeficiencyresourcenGaltmutation-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nHEXAdb-HumanHexosaminidaseAmutationdb(Tay-sachsdisease)nIL2RGbase-HumanIL2RG(Interleukin-2receptorgamma)mutationdb(X-SCID)nL1CAMmutation-HumanL1CAMmutationdbnLDLRmutation-HumanLDLRmutationdb(Familialhypercholesterolemia)nLQTSdb-LongQTsyndromedbnNCF1base-HumanNCF1mutationdbnNCF2base-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nNeuromusculardiseaseswebsitenNCL-NeuronalCeroidLipofuscinosesmutationdbnOTCase-Humanornithinetranscarbamylase(OTCase)websitenCytochromeP450allelesnomenclaturenp53mutationdb-UniversityofTokyop53mutationdbnGermlinep53mutationdb-UniversityofPraguedbofgermlinep53mutationsnPAHdb-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nPAX6mutation-HumanPAX6mutationdbnPrion-PrionandpriondiseasewebsitenRAG1base-HumanRAG1mutationdbnRAG2base-HumanRAG2mutationdbnRB1base-Humanretinoblastoma-associatedprotein(RB)mutationdbnRetNet-RetinalInformationNetworknRetinaInternationalScientificNewsletter-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nTSC-TSC(TSC1/TSC2)variationdbnTSC2-Cardiff-RotterdamTuberousSclerosis(TS)db(Tuberin;TSC2)nTGDB-TumorgenedbnVMD2mutation-HumanVMD2mutationdbnvWFmutation-HumanvonWillebrandfactor(vWF)mutationdbnWRN-HumanWRNmutationdb(Warnerdisease)nWT1mutation-HumanWT1mutationdbnX-ALDmutation-HumanABCD1mutationdb第32页进化相关数据库及资源进化相关数据库及资源nClustersofOrthologousGroups(COG)-Phylogeneticclassificationofproteinsfrom21completegenomesnXREFdb-Cross-referencingofmodelorganismgeneticswithmammalianphenotypesnTreeBASE-RelationaldbofphylogeneticinformationnTheTreeoflife-CollectionofWWWpagesonphylogenyandbiodiversityoforganisms第33页专利数据库专利数据库nDPD-DNAPatentdbnAgPatents-AgriculturalBiotechnologypatentsfromtheUSDAnUSPTOpatentdb-USAPatentandTrademarkOfficepatentdbnEspcenet-PatentinformationdatabasefromtheEuropeanPatentOffice(worldwidecoverage)nTheDelphionIntellectualPropertyNetwork(IPN)forsearching,viewing,andanalyzingpatentdocuments.第34页资源目录服务器或网页资源目录服务器或网页nBioCatalog-TheBioCatalogatEBInYellowBAGI-BioAccessGuidetotheInternetatHoustonUniversitynSoftwarelibraryfromGnDBCAT-DatabasescatalogatINFOBIOGENnMBDL-MolecularBiologyDatabaseListnAmosWWWlinkspagenNucleicAcidsResearchdatabaseissue第35页HumannCEPH-genotypedatabasenCEPHhomepage-aresearchlaboratorywhichconstructsmapsofthehumangenomenGeneMap99-AGeneMapoftheHumanGenome(NCBI)nOMIM-OnlineMendelianInheritanceinMannGENATLAS-HumangenesatlasnGeneClinics-MedicalgeneticsknowledgebasenGDB-HumangenesandgenomicmapsnGeneCards-Dbintegratinginformationonhumangenes第36页HumannUDB-UnifieddbforHumangenomemappingnEnsembl-HumangenomeannotationssitenUCSChumangenomeworkingdraftnTIGRHGI-TIGRHumanGeneIndexnHumanBACEndsDatabase-Non-redundanthumanBACendsequencesnHsUniGene-HumantranscriptsinGenBank(ESTclusters)nSTACK-SequenceTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)第37页HumannAllgenes.org-Humanpredictedgeneindex/catalognGenLink-HumangeneticsresourcenGENOTK-HumancDNAdbnHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)nCGAP-CancerGenomeAnatomyProjectnSCDb-Stemcelldb第38页HumannHuGeMap-HumangenomegeneticandphysicalmapdatanG3-RH-StanfordG3andTNGradiationhybridmapsnGB4-RH-Genebridge4(GB4)humanradiationhybridmapsnRadiationHybridDatabase-Radiationhybridmapdata第39页Humanchromosome18nChr1-Humanchromosome1atRockefellerUniversityMirroratEBInChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenternChr7-Humanchromosome7dbatOntariosHospitalforSickChildrennChr8SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome8第40页Humanchromosome911nChr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9nChr9-Humanchromosome9dbnChr10SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10nGTCChr10data-Humanchromosome10datafromGenomeTherapeuticsCorporationnChr11SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome11n11DB-Humanchromosome11dbatImperialCollege(U.K.)第41页Humanchromosome1216nChr12SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome12nChr13-Humanchromosome13dbatColumbianChr14SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome14nChr15SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome15nChr15UBC-Humanchromosome15WWWpageatUBCnChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16第42页Humanchromosome1619nChr16LANL-Humanchromosome16dbatLosAlamosNationalLaboratorynChr16TIGR-Humanchromosome16dbatTIGRnChr17SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome17nChr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18nChr18-Humanchromosome18atBostonChildrensHospitalnChr19SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19第43页Humanchromosome2022nChr20SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome20nChr21SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21nChr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)nChr21atERI-Humanchromosome21genomicsequencedbfromtheEleanorRooseveltInstitutenChr22SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome22nChr22atSanger-SangerCenterchromosome22projectnChr22atHGC-Humangenomecenterforchromosome22第44页HumanchromosomeXYnChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXnIXDB-IntegratedXchromosomedbnChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeYnnDRESH-HumancDNAcloneshomologoustoDrosophilamutantgenes第45页VertebratesnOMIA-OnlineMendelianInheritanceinAnimalsnMGI-MouseGenomeInformatics(includesMouseGenomeDatabase(MGD)MirrorsinAustralia|UK|JapannTIGRMGI-TIGRMouseGeneIndexnMmUniGene-MousetranscriptsinGenBank(ESTclusters)nRatMAP-RatgenomedbnTIGRRGI-TIGRRatGeneIndexnRnUnigene-RattranscriptsinGenBank(ESTclusters)第46页VertebratesnBovBASE-Bovinegenomedb(inUK)nBOVMAP-Bovinegenomedb(inFrance)nArk-Cat-CatgenomedbnHorseBASE-HorsegenomedbnDGP-DogGenomeProjectnPiGBASE-PiggenomedbnSheepBASE-Sheepgenomedb(alsoknownasSheepMap)MirrorinUKnMIS-MendelianInheritanceinSheepnChickGBASE-Chickengenomedb第47页VertebratesnFugu-HGMPResourceCentreFuguProject(Fugurubripes)nMedakafish-Mekadafish(Oryziaslatipes)servernArk-Tilapia-TilapiamossambicagenomedbnThefishnet-ZebrafishservernFishBase-Globalinformationsystemonfishes第48页MitochondrionandchloroplastnGOBASE-OrganelleGenomeDatabasenMitoDat-MendelianInheritanceandtheMitochondriondb(mitochondrialnucleargenes)nMITOMAP-HumanmitochondrialgenomedbnMmtDB-MetazoamitochondrialDNAvariantsdbnMitBASE-IntegratedmitochondrialDNAdbnMitBASE-Pilot-DbofS.cerevisiaenucleargenesinvolvedinmitochondrialbiogenesisnHvrBase-PrimatesmtDNAcontrolregionsequencescompilation第49页MitochondrionandchloroplastnMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)nMITOP-Mitochondrialproteins,genesanddiseasesnAMmtDB-MetazoanmitochondrialDNAsequences第50页InsectsnDrosophilaSWISS-PROTlist-LinkstoDrosophilaSWISS-PROTentriesnFlyBase-DrosophilageneticandmoleculardbMirroratEBInFlyView-DrosophilaimagedbnGIFTS-GeneInteractionsintheFlyTrans-WorldServernFlyNets-DbofmolecularinteractionsinDrosophilamelanogasternSOS-DGBD-DbofDrosophilaDNAsequencesannotatedwithregulatorybindingsitesnMosquitoGenomics第51页InvertebratesnWormBase-C.elegansdbMirroratSangernC.elegansWWWserver-atUniversityofTexasSouthwesternnACeDb-CaenorhabditiselegansdbnC.elegansMitochondrialDirectory-DataonC.elegansgenesformitochondrialproteinsnC.elegansEST-C.elegansESTdbfromJapan(YujiKoharasgroup)nC.elegansSWISS-PROTlist-LinkstoC.elegansSWISS-PROTentriesnWormPep-C.elegansproteinsdbnWormPD-C.elegansproteindb第52页InvertebratesnDictysteliumGenomeSequencingprojectatBCMnDictyosteliumdiscoideumgenomeprojectatIENAnDictyDb-DictyosteliumdiscoideumdbnDicty_cDB-DictyosteliumdiscoideumcDNAprojec