生物信息学相关数据库资源介绍教学内容.ppt

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1、生物信息学相关数据库资源介绍一、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我国的核酸序列公共数据库ndbEST-DatabaseofExpressedSequenceTags(NCBI)ndbSTS-DatabaseofSequenceTaggedSites(NCBI)2.基因组及相关数据库GenomicDatabas

2、esnGenomeWeb(HGMP)-AcatalogueofusefulWebsitesforGenomicswithasetofcollectionsofgenomedatabasesnGSDB-GenomeSequencedatabase(NCGR)nGOLD-GenomesOn-linedbn一些数据库的直接链接3.核酸三维结构数据库nNDB-NucleicAcidDatabank(3Dstructures)nBNASDB-NucleicacidstructuredbfromUniversityofPune4.其他nAsDb-AberrantSplicingdbnACUTS-Ancie

3、ntconserveduntranslatedDNAsequencesdbnCodonUsageDb-ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.nEPD-EukaryoticPromoterdbnHOVERGEN-HomologousVertebrateGenesdbnIMGT-ImMunoGeneTicsdbMirroratEBInISIS-IntronSequenceandInformationSystemnRDP-RibosomaldbProjectngRNAsdb-Gu

4、ideRNAdbnPLACE-Plantcis-actingregulatoryDNAelementsdb其它其它nPlantCARE-Plantcis-actingregulatoryDNAelementsdbnsRNAdb-SmallRNAdbnssurRNA-SmallribosomalsubunitdbnlsurRNA-Largeribosomalsubunitdbn5SrRNA-5SribosomalRNAdbntmRNAWebsitentmRDB-tmRNAdBntRNA-tRNAcompilationfromtheUniversityofBayreuthnuRNADB-uRNAd

5、b其他其他nRNAediting-RNAeditingsitenRNAmoddb-RNAmodificationdbnTelDB-MultimediaTelomereResourcenTRADAT-TRAnscriptionDatabasesandAnalysisToolsnSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)TransgenicsnCreTransgenicDatabase-CretransgenicmouselinesnTransgenic/TargetedMutationDatabase-Informationon

6、transgenicanimalsandtargetedmutations二.蛋白质序列和相关数据库nSWISS-PROT-SWISS-PROTannotatedproteinsequencedbnPIR-international-TheProteinInformationResource(proteinsequence)nMIPS-Martinsriedinstituteforproteinsequenceandhomologydataandyeastgenomeinformation蛋白质及其相关数据库蛋白质及其相关数据库nPROSITE-PROSITEdictionaryofprote

7、insitesandpatternsnInterPro-IntegratedResourcesofProteinsDomainsandFunctionalSitesnBLOCKS-BLOCKSdbnDOMO-Proteindomaindb(Automaticallygenerated)nPfam-Proteinfamiliesdb(HMMderived)MirroratSangernPRINTS-ProteinMotiffingerprintdbnProDom-Proteindomaindb(Automaticallygenerated)nPROTOMAP-Anautomatichierarc

8、hicalclassificationofSWISS-PROTproteinsnSBASE-SBASEdomaindb(Proteindomainsequencelibrary)nSMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)nProClass-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nPDB-ProteinDataBankMirrorsi

9、nEBInBioMagResBank-Repositoryfordataonproteins,peptides,andnucleicacidsfromNMRspectroscopynSWISS-MODELRepository-AutomaticallygeneratedproteinmodelsdbnModBase-DbofcomparativeproteinstructuremodelsnCATH-UCLBSMstructuralclassificationofproteinsnSCOP-StructuralclassificationofproteinsMirroratUSA|Israel

10、|Singapore|AustralianMol_R_Us-MoleculesRUs,browserforPDBnBMMDomainServer-BiomolecularModellingLaboratory(ICRF)proteindomainservernPRESAGE-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nSBASE-SBASEdomaindb(Proteindomainsequencelibrary)nSMART-Proteinsignallingandextracellulardoma

11、inpatterns(SimpleModularArchitectureResearchTool)nProClass-ProteinsequencealignmentsandcurationofproteinfamiliesnKabat-KabatdbofproteinofimmunologicalinterestnPMD-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nWORLD-2DPAGE-Acompleteindexof2D-PAGEdbandserversnPhoretixlinks-Phoretixpageoflinksto2Dgeldb三、信号传导

12、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五、特定基因或

13、蛋白质的数据库五、特定基因或蛋白质的数据库nAAA-AAAfamilyofATPasesserverAcetylcholinesterasesnALDH-AldehydedehydrogenasegenesuperfamilydbnAminoacyl-tRNAsynthetasesinSWISS-PROT-Listofaminoacyl-tRNAsynthetasesinSWISS-PROTnAARSDB-Aminoacyl-tRNAsynthetasesdbnAllergensinSWISS-PROT-NomenclatureandindexofallergensinSWISS-PROT特定

14、基因或蛋白质的数据库特定基因或蛋白质的数据库nAMSDb-AntimicrobialsequencesdbnAntibodyresourcepage-LinkstoantibodyrelatedWebresourcesnAustralianvenomandtoxindbnBacillusthuringiensistoxinspecificitydbnTFII-BasaltranscriptionfactorsnBloodgroupantigensinSWISS-PROTnBCGD-BreastcancergenesdbfromMBCRnBRENDA-Dbofenzymefunctionalda

15、ta特定基因或蛋白质的数据库特定基因或蛋白质的数据库nEF-handCaBP-EF-handcalcium-bindingproteinsdbnCAZy-Carbohydrate-ActiveenZYmesWebsitenCBSdomain-CystathionineBetaSynthasedomainWWWpagenCDantigensinSWISS-PROT-Nomenclatureforsurfaceproteinsofhumanleucocytes(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nCDantigensinPROW-Databaseoninformationabo

16、utCDantigensnChaperonin-InformationonGroELandGroESchaperoninsnConotoxins-InformationonconotoxinsfromaWebsiteonconeshells。etc。糖类相关数据库糖类相关数据库nCarbBank-ComplexCarbohydrateStructureDatabaseGlycoSuiteDB-DbofglycanstructuresnTGN-TheGlycoscienceNetworknFCCA-ForumCarbohydratesComingofAgenCARBHYD-Carbohydrat

17、einformationWWWsitesnMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides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基因表达数据库基因表达数据库nASDB-Proteinproductsandexpressionpatternsofalternatively-splicedge

18、nesnAxeldb-GeneexpressioninXenopusnBodyMap-HumanandmousegeneexpressiondatanEpoDB-GenesexpressedinvertebrateRBCnFlyView-DrosophiladevelopmentandgeneticsnGeneExpressionDatabase(GXD)-MousegeneexpressionandgenomicsnKidneyDevelopmentDatabase-Kidneydevelopmentandgeneexpression基因表达数据库基因表达数据库nMAGEST-Ascidia

19、n(Halocynthiaroretzi)geneexpressionpatternsnMouseAtlasandGeneExpressionDatabase-Spatially-mappedgeneexpressiondatanPEDB-NormalandaberrantprostategeneexpressionnToothDevelopmentDatabase-GeneexpressionindentaltissuenTRIPLES-TRansposon-InsertionPhenotypes,LocalizationandExpressioninSaccharomyces人类基因突变及

20、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)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(Mutationsinhu

21、mangenescausingalbinism)Alpha-glucosidase-Informationabouthumanacidalpha-glucosidase(GSD-II)nARmutations-HumanandrogenreceptormutationdbnAntithrombinmutationdbnAsthmaandAllergygenedbnBIOMDB-DbofmutationscausingtetrahydrobiopterindeficienciesnBLMbase-HumanBLMmutationdb(Bloomsnydrom)人类基因突变及疾病相关数据库人类基因

22、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人类基因突变及疾

23、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-phosphateuridylyltransferasemu

24、tationdb(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nHEXAdb-HumanHexosaminidaseAmutationdb(Tay-sachsdisease)nIL2RGbase-HumanIL2RG(Interleukin-2receptorgamma)mutationdb(X-SCID)nL1CAMmutation-HumanL1CAMmutationdbnLDLRmutation-HumanLDLRmutationdb(Familialhypercholesterolemia)nLQTSdb-LongQTsyndromedbnNCF1

25、base-HumanNCF1mutationdbnNCF2base-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nNeuromusculardiseaseswebsitenNCL-NeuronalCeroidLipofuscinosesmutationdbnOTCase-Humanornithinetranscarbamylase(OTCase)websitenCytochromeP450allelesnomenclaturenp53mutationdb-UniversityofTokyop53mutationdbnGermlinep53mut

26、ationdb-UniversityofPraguedbofgermlinep53mutationsnPAHdb-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nPAX6mutation-HumanPAX6mutationdbnPrion-PrionandpriondiseasewebsitenRAG1base-HumanRAG1mutationdbnRAG2base-HumanRAG2mutationdbnRB1base-Humanretinoblastoma-associatedprotein

27、(RB)mutationdbnRetNet-RetinalInformationNetworknRetinaInternationalScientificNewsletter-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nTSC-TSC(TSC1/TSC2)variationdbnTSC2-Cardiff-RotterdamTuberousSclerosis(TS)db(Tuberin;TSC2)nTGDB-TumorgenedbnVMD2mutation-HumanVMD2mutationd

28、bnvWFmutation-HumanvonWillebrandfactor(vWF)mutationdbnWRN-HumanWRNmutationdb(Warnerdisease)nWT1mutation-HumanWT1mutationdbnX-ALDmutation-HumanABCD1mutationdb进化相关数据库及资源进化相关数据库及资源nClustersofOrthologousGroups(COG)-Phylogeneticclassificationofproteinsfrom21completegenomesnXREFdb-Cross-referencingofmodel

29、organismgeneticswithmammalianphenotypesnTreeBASE-RelationaldbofphylogeneticinformationnTheTreeoflife-CollectionofWWWpagesonphylogenyandbiodiversityoforganisms专利数据库专利数据库nDPD-DNAPatentdbnAgPatents-AgriculturalBiotechnologypatentsfromtheUSDAnUSPTOpatentdb-USAPatentandTrademarkOfficepatentdbnEspcenet-Pa

30、tentinformationdatabasefromtheEuropeanPatentOffice(worldwidecoverage)nTheDelphionIntellectualPropertyNetwork(IPN)forsearching,viewing,andanalyzingpatentdocuments.资源目录服务器或网页资源目录服务器或网页nBioCatalog-TheBioCatalogatEBInYellowBAGI-BioAccessGuidetotheInternetatHoustonUniversitynSoftwarelibraryfromGnDBCAT-Da

31、tabasescatalogatINFOBIOGENnMBDL-MolecularBiologyDatabaseListnAmosWWWlinkspagenNucleicAcidsResearchdatabaseissueHumannCEPH-genotypedatabasenCEPHhomepage-aresearchlaboratorywhichconstructsmapsofthehumangenomenGeneMap99-AGeneMapoftheHumanGenome(NCBI)nOMIM-OnlineMendelianInheritanceinMannGENATLAS-Humang

32、enesatlasnGeneClinics-MedicalgeneticsknowledgebasenGDB-HumangenesandgenomicmapsnGeneCards-DbintegratinginformationonhumangenesHumannUDB-UnifieddbforHumangenomemappingnEnsembl-HumangenomeannotationssitenUCSChumangenomeworkingdraftnTIGRHGI-TIGRHumanGeneIndexnHumanBACEndsDatabase-Non-redundanthumanBACe

33、ndsequencesnHsUniGene-HumantranscriptsinGenBank(ESTclusters)nSTACK-SequenceTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)HumannAllgenes.org-Humanpredictedgeneindex/catalognGenLink-HumangeneticsresourcenGENOTK-HumancDNAdbnHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)nCGAP-

34、CancerGenomeAnatomyProjectnSCDb-StemcelldbHumannHuGeMap-HumangenomegeneticandphysicalmapdatanG3-RH-StanfordG3andTNGradiationhybridmapsnGB4-RH-Genebridge4(GB4)humanradiationhybridmapsnRadiationHybridDatabase-RadiationhybridmapdataHumanchromosome18nChr1-Humanchromosome1atRockefellerUniversityMirroratE

35、BInChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenternChr7-Humanchromosome7dbatOntariosHospitalforSickChildrennChr8SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome8Humanchromosome911nChr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9nChr9-Humanchromosome9dbnChr10

36、SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10nGTCChr10data-Humanchromosome10datafromGenomeTherapeuticsCorporationnChr11SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome11n11DB-Humanchromosome11dbatImperialCollege(U.K.)Humanchromosome1216nChr12SWISS-PROTlist-LinkstoSWISS-PROTe

37、ntriesfromhumanchromosome12nChr13-Humanchromosome13dbatColumbianChr14SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome14nChr15SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome15nChr15UBC-Humanchromosome15WWWpageatUBCnChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16

38、Humanchromosome1619nChr16LANL-Humanchromosome16dbatLosAlamosNationalLaboratorynChr16TIGR-Humanchromosome16dbatTIGRnChr17SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome17nChr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18nChr18-Humanchromosome18atBostonChildrensHospitalnChr1

39、9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19Humanchromosome2022nChr20SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome20nChr21SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21nChr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)nChr21atERI-Humanchromosome21geno

40、micsequencedbfromtheEleanorRooseveltInstitutenChr22SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome22nChr22atSanger-SangerCenterchromosome22projectnChr22atHGC-Humangenomecenterforchromosome22HumanchromosomeXYnChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXnIXDB-IntegratedXc

41、hromosomedbnChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeYnnDRESH-HumancDNAcloneshomologoustoDrosophilamutantgenesVertebratesnOMIA-OnlineMendelianInheritanceinAnimalsnMGI-MouseGenomeInformatics(includesMouseGenomeDatabase(MGD)MirrorsinAustralia|UK|JapannTIGRMGI-TIGRMouseGeneIndexnMm

42、UniGene-MousetranscriptsinGenBank(ESTclusters)nRatMAP-RatgenomedbnTIGRRGI-TIGRRatGeneIndexnRnUnigene-RattranscriptsinGenBank(ESTclusters)VertebratesnBovBASE-Bovinegenomedb(inUK)nBOVMAP-Bovinegenomedb(inFrance)nArk-Cat-CatgenomedbnHorseBASE-HorsegenomedbnDGP-DogGenomeProjectnPiGBASE-PiggenomedbnSheep

43、BASE-Sheepgenomedb(alsoknownasSheepMap)MirrorinUKnMIS-MendelianInheritanceinSheepnChickGBASE-ChickengenomedbVertebratesnFugu-HGMPResourceCentreFuguProject(Fugurubripes)nMedakafish-Mekadafish(Oryziaslatipes)servernArk-Tilapia-TilapiamossambicagenomedbnThefishnet-ZebrafishservernFishBase-Globalinforma

44、tionsystemonfishesMitochondrionandchloroplastnGOBASE-OrganelleGenomeDatabasenMitoDat-MendelianInheritanceandtheMitochondriondb(mitochondrialnucleargenes)nMITOMAP-HumanmitochondrialgenomedbnMmtDB-MetazoamitochondrialDNAvariantsdbnMitBASE-IntegratedmitochondrialDNAdbnMitBASE-Pilot-DbofS.cerevisiaenucl

45、eargenesinvolvedinmitochondrialbiogenesisnHvrBase-PrimatesmtDNAcontrolregionsequencescompilationMitochondrionandchloroplastnMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)nMITOP-Mitochondrialproteins,genesanddiseasesnAMmtDB-MetazoanmitochondrialDNAsequencesInsectsnDrosophilaSWISS-P

46、ROTlist-LinkstoDrosophilaSWISS-PROTentriesnFlyBase-DrosophilageneticandmoleculardbMirroratEBInFlyView-DrosophilaimagedbnGIFTS-GeneInteractionsintheFlyTrans-WorldServernFlyNets-DbofmolecularinteractionsinDrosophilamelanogasternSOS-DGBD-DbofDrosophilaDNAsequencesannotatedwithregulatorybindingsitesnMos

47、quitoGenomicsInvertebratesnWormBase-C.elegansdbMirroratSangernC.elegansWWWserver-atUniversityofTexasSouthwesternnACeDb-CaenorhabditiselegansdbnC.elegansMitochondrialDirectory-DataonC.elegansgenesformitochondrialproteinsnC.elegansEST-C.elegansESTdbfromJapan(YujiKoharasgroup)nC.elegansSWISS-PROTlist-L

48、inkstoC.elegansSWISS-PROTentriesnWormPep-C.elegansproteinsdbnWormPD-C.elegansproteindbInvertebratesnDictysteliumGenomeSequencingprojectatBCMnDictyosteliumdiscoideumgenomeprojectatIENAnDictyDb-DictyosteliumdiscoideumdbnDicty_cDB-DictyosteliumdiscoideumcDNAprojectnConeshellsWebsitenParasitegenomesdban

49、dresourcesnParasitegenomesWWWsitenPlasmoDB-P.falciparumgenomedbInvertebratesnMalaria-WHO-Malariadb(fromWHO)（疟疾nue）nP.falciparumSanger-P.falciparumgenomeprojectatSangernPFDB-PlasmodiumfalciparumGenomedb（疟原虫）nP.falciparum-PlasmodiumfalciparumGeneSequenceTagprojectInvertebratesnMAD-MalariaAntigendbnMal

50、ariaparasitemetabolicpathwaysnLGN-LeishmaniaGenomeNetworknTrypanosomabruceigenomeprojectnTrypanosomacruzigenomeprojectnkDNA-KinetoplastMinicircleSequencedbPlantsnNAL-AGIS-AccesstomanyplantgenomedatabasesattheNationalAgriculturalLibrarynDemetersgenomes-AccesstomanyplantgenomedatabasesattheUSDA-ARSnMe