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1、生物信息学资源库介绍第1页，本讲稿共80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 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）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）基因或蛋白质一些特定数据库糖类及其相关数据库蛋白质翻译后修饰相关数据库基因表达数据库人类基因突变及疾病相关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，本讲稿共80页核酸及其相关数据库核酸及其相关数据库 核酸序列数据库核酸序列数据库BIOSINO我
2、国的核酸序列公共数据库EMBL-EMBLNucleotidesequencedatabase(EBI)*GenBank-GenBankNucleotideSequencedatabase(NCBI)*DDBJ-DNADataBankofJapan*dbEST-DatabaseofExpressedSequenceTags(NCBI)dbSTS-DatabaseofSequenceTaggedSites(NCBI)第3页，本讲稿共80页2.基因组及相关数据库 Genomic DatabasesGenomeWeb(HGMP)-AcatalogueofusefulWebsitesforGenomic
3、swithasetofcollectionsofgenomedatabasesGSDB-GenomeSequencedatabase(NCGR)GOLD-GenomesOn-linedb一些数据库的直接链接第4页，本讲稿共80页3.核酸三维结构数据库NDB-NucleicAcidDatabank(3Dstructures)BNASDB-NucleicacidstructuredbfromUniversityofPune第5页，本讲稿共80页4.其他AsDb-AberrantSplicingdbACUTS-AncientconserveduntranslatedDNAsequencesdbCod
4、onUsageDb-ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.EPD-EukaryoticPromoterdbHOVERGEN-HomologousVertebrateGenesdbIMGT-ImMunoGeneTicsdbMirroratEBIISIS-IntronSequenceandInformationSystemRDP-RibosomaldbProjectgRNAsdb-GuideRNAdbPLACE-Plantcis-actingregulatoryDNAeleme
5、ntsdb第6页，本讲稿共80页其它其它PlantCARE-Plantcis-actingregulatoryDNAelementsdbsRNAdb-SmallRNAdbssurRNA-SmallribosomalsubunitdblsurRNA-Largeribosomalsubunitdb5SrRNA-5SribosomalRNAdbtmRNAWebsitetmRDB-tmRNAdBtRNA-tRNAcompilationfromtheUniversityofBayreuthuRNADB-uRNAdb第7页，本讲稿共80页其他其他RNAediting-RNAeditingsiteRNAmo
6、ddb-RNAmodificationdbTelDB-MultimediaTelomereResourceTRADAT-TRAnscriptionDatabasesandAnalysisToolsSubviralRNAdb-SmallcircularRNAsdb(viroidandviroid-like)第8页，本讲稿共80页TransgenicsCreTransgenicDatabase-CretransgenicmouselinesTransgenic/TargetedMutationDatabase-Informationontransgenicanimalsandtargetedmut
7、ations第9页，本讲稿共80页1.蛋白质序列和相关数据库SWISS-PROT-SWISS-PROTannotatedproteinsequencedbPIR-international-TheProteinInformationResource(proteinsequence)MIPS-Martinsriedinstituteforproteinsequenceandhomologydataandyeastgenomeinformation第10页，本讲稿共80页蛋白质及其相关数据库蛋白质及其相关数据库 PROSITE-PROSITEdictionaryofproteinsitesandp
8、atternsInterPro-IntegratedResourcesofProteinsDomainsandFunctionalSitesBLOCKS-BLOCKSdbDOMO-Proteindomaindb(Automaticallygenerated)Pfam-Proteinfamiliesdb(HMMderived)MirroratSangerPRINTS-ProteinMotiffingerprintdbProDom-Proteindomaindb(Automaticallygenerated)PROTOMAP-Anautomatichierarchicalclassificatio
9、nofSWISS-PROTproteinsSBASE-SBASEdomaindb(Proteindomainsequencelibrary)SMART-Proteinsignallingandextracellulardomainpatterns(SimpleModularArchitectureResearchTool)ProClass-Proteinsequencealignmentsandcurationofproteinfamilies第11页，本讲稿共80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PDB-ProteinDataBankMirrorsinEBIBioMag
10、ResBank-Repositoryfordataonproteins,peptides,andnucleicacidsfromNMRspectroscopySWISS-MODELRepository-AutomaticallygeneratedproteinmodelsdbModBase-DbofcomparativeproteinstructuremodelsCATH-UCLBSMstructuralclassificationofproteinsSCOP-StructuralclassificationofproteinsMirroratUSA|Israel|Singapore|Aust
11、raliaMol_R_Us-MoleculesRUs,browserforPDBBMMDomainServer-BiomolecularModellingLaboratory(ICRF)proteindomainserverPRESAGE-Collaborativeresourceforstructuralgenomics第12页，本讲稿共80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 SBASE-SBASEdomaindb(Proteindomainsequencelibrary)SMART-Proteinsignallingandextracellulardomainpatte
12、rns(SimpleModularArchitectureResearchTool)ProClass-ProteinsequencealignmentsandcurationofproteinfamiliesKabat-KabatdbofproteinofimmunologicalinterestPMD-ProteinMutantdb第13页，本讲稿共80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WORLD-2DPAGE-Acompleteindexof2D-PAGEdbandserversPhoretixlinks-Phoretixpageoflinksto2Dgeldb第14页，本
13、讲稿共80页信号传导及蛋白质信号传导及蛋白质-蛋白质相互作用相蛋白质相互作用相关数据库关数据库DIP-DbofInteractingProteinsINTERACT-Protein-ProteininteractiondbProNet-Protein-ProteininteractiondbCANSITE-SignalTransductionsWebSPAD-SignalingpathwaydbCSNDB-CellSignalingNetworksdb第15页，本讲稿共80页DNA和蛋白质相互作用数据库和蛋白质相互作用数据库DPInteract-DNA-Proteinsinteractions
14、db第16页，本讲稿共80页特定基因或蛋白质的数据库特定基因或蛋白质的数据库AAA-AAAfamilyofATPasesserverAcetylcholinesterasesALDH-AldehydedehydrogenasegenesuperfamilydbAminoacyl-tRNAsynthetasesinSWISS-PROT-Listofaminoacyl-tRNAsynthetasesinSWISS-PROTAARSDB-Aminoacyl-tRNAsynthetasesdbAllergensinSWISS-PROT-Nomenclatureandindexofallergensin
15、SWISS-PROT第17页，本讲稿共80页特定基因或蛋白质的数据库特定基因或蛋白质的数据库AMSDb-AntimicrobialsequencesdbAntibodyresourcepage-LinkstoantibodyrelatedWebresourcesAustralianvenomandtoxindbBacillusthuringiensistoxinspecificitydbTFII-BasaltranscriptionfactorsBloodgroupantigensinSWISS-PROTBCGD-BreastcancergenesdbfromMBCRBRENDA-Dbofen
16、zymefunctionaldata第18页，本讲稿共80页特定基因或蛋白质的数据库特定基因或蛋白质的数据库EF-handCaBP-EF-handcalcium-bindingproteinsdbCAZy-Carbohydrate-ActiveenZYmesWebsiteCBSdomain-CystathionineBetaSynthasedomainWWWpageCDantigensinSWISS-PROT-Nomenclatureforsurfaceproteinsofhumanleucocytes(CD)第19页，本讲稿共80页特定基因或蛋白质的数据库特定基因或蛋白质的数据库CDanti
17、gensinPROW-DatabaseoninformationaboutCDantigensChaperonin-InformationonGroELandGroESchaperoninsConotoxins-InformationonconotoxinsfromaWebsiteonconeshells。etc。第20页，本讲稿共80页糖类相关数据库糖类相关数据库CarbBank-ComplexCarbohydrateStructureDatabaseGlycoSuiteDB-DbofglycanstructuresTGN-TheGlycoscienceNetworkFCCA-ForumCa
18、rbohydratesComingofAgeCARBHYD-CarbohydrateinformationWWWsitesMonosacharidebrowser-SpacefillingFischerprojectionformonosaccharides第21页，本讲稿共80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 O-GlycBase-O-glycosylatedproteinsdbPhosphoBase-PhosphorylationsitesdbRESID-DbofAminoAcidModifications第22页，本讲稿共80页基因表达数据库基因表达数据库 ASDB
19、-Proteinproductsandexpressionpatternsofalternatively-splicedgenesAxeldb-GeneexpressioninXenopusBodyMap-HumanandmousegeneexpressiondataEpoDB-GenesexpressedinvertebrateRBCFlyView-DrosophiladevelopmentandgeneticsGeneExpressionDatabase(GXD)-MousegeneexpressionandgenomicsKidneyDevelopmentDatabase-Kidneyd
20、evelopmentandgeneexpression第23页，本讲稿共80页基因表达数据库基因表达数据库 MAGEST-Ascidian(Halocynthiaroretzi)geneexpressionpatternsMouseAtlasandGeneExpressionDatabase-Spatially-mappedgeneexpressiondataPEDB-NormalandaberrantprostategeneexpressionToothDevelopmentDatabase-GeneexpressionindentaltissueTRIPLES-TRansposon-Ins
21、ertionPhenotypes,LocalizationandExpressioninSaccharomyces第24页，本讲稿共80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HMGD-HumanGeneMutationdbSVD-SequencevariationdbHGBASE-HumanGenicBi-AllelicSequencesdbTheSNPconsortiumdbSNP-Humansinglenucleotidepolymorphism(SNP)dbListofmutationdatabasesfromOMIMListofmutationdatabasesfr
22、omIMT(Finland)第25页，本讲稿共80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ADB-Albinismdb(Mutationsinhumangenescausingalbinism)Alpha-glucosidase-Informationabouthumanacidalpha-glucosidase(GSD-II)ARmutations-HumanandrogenreceptormutationdbAntithrombinmutationdbAsthmaandAllergygenedbBIOMDB-Dbofmutationscausingtetrahydrobi
23、opterindeficienciesBLMbase-HumanBLMmutationdb(Bloomsnydrom)第26页，本讲稿共80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BTKbase-HumanBTKmutationdb(X-linkedagammaglobulinemia)CD40Lbase-HumanCD40ligandmutationdbCOL1/3mutation-HumanTypeIandIIIcollagenmutationdbCFTRmutation-Humancysticfibrosismutationdb(CFTR)EMDdb-HumanEmer
24、in(EMD)mutationdb(Emery-Dreifussmusculardystrophy)KMeyeDB-Eyediseasegenesdb第27页，本讲稿共80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FVIImutation-HumanFactorVIImutationdbHAMSTeRS-HumanFactorVIIImutationdb(HaemophiliaA)HAeMB-HumanFactorIXmutationdb(HaemophiliaB)FBN1mutation-Humanfibrillin1mutationdb(Marfansyndrome)G6P
25、D-HumanG6PDdeficiencyresourceGaltmutation-Humangalactose-1-phosphateuridylyltransferasemutationdb(Galactosemia)第28页，本讲稿共80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HEXAdb-HumanHexosaminidaseAmutationdb(Tay-sachsdisease)IL2RGbase-HumanIL2RG(Interleukin-2receptorgamma)mutationdb(X-SCID)L1CAMmutation-HumanL1CAMmuta
26、tiondbLDLRmutation-HumanLDLRmutationdb(Familialhypercholesterolemia)LQTSdb-LongQTsyndromedbNCF1base-HumanNCF1mutationdbNCF2base-HumanNCF2mutationdb第29页，本讲稿共80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NeuromusculardiseaseswebsiteNCL-NeuronalCeroidLipofuscinosesmutationdbOTCase-Humanornithinetranscarbamylase(OTCas
27、e)websiteCytochromeP450allelesnomenclaturep53mutationdb-UniversityofTokyop53mutationdbGermlinep53mutationdb-UniversityofPraguedbofgermlinep53mutationsPAHdb-Humanphenylalaninehydroxylase(PAH)mutationdb第30页，本讲稿共80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PAX6mutation-HumanPAX6mutationdbPrion-Prionandpriondiseasewe
28、bsiteRAG1base-HumanRAG1mutationdbRAG2base-HumanRAG2mutationdbRB1base-Humanretinoblastoma-associatedprotein(RB)mutationdbRetNet-RetinalInformationNetworkRetinaInternationalScientificNewsletter-InformationonRetinalgenes,proteinsanddiseases第31页，本讲稿共80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TSC-TSC(TSC1/TSC2)varia
29、tiondbTSC2-Cardiff-RotterdamTuberousSclerosis(TS)db(Tuberin;TSC2)TGDB-TumorgenedbVMD2mutation-HumanVMD2mutationdbvWFmutation-HumanvonWillebrandfactor(vWF)mutationdbWRN-HumanWRNmutationdb(Warnerdisease)WT1mutation-HumanWT1mutationdbX-ALDmutation-HumanABCD1mutationdb第32页，本讲稿共80页进化相关数据库及资源进化相关数据库及资源 Cl
30、ustersofOrthologousGroups(COG)-Phylogeneticclassificationofproteinsfrom21completegenomesXREFdb-Cross-referencingofmodelorganismgeneticswithmammalianphenotypesTreeBASE-RelationaldbofphylogeneticinformationTheTreeoflife-CollectionofWWWpagesonphylogenyandbiodiversityoforganisms第33页，本讲稿共80页专利数据库专利数据库 DP
31、D-DNAPatentdbAgPatents-AgriculturalBiotechnologypatentsfromtheUSDAUSPTOpatentdb-USAPatentandTrademarkOfficepatentdbEspcenet-PatentinformationdatabasefromtheEuropeanPatentOffice(worldwidecoverage)TheDelphionIntellectualPropertyNetwork(IPN)forsearching,viewing,andanalyzingpatentdocuments.第34页，本讲稿共80页资
32、源目录服务器或网页资源目录服务器或网页BioCatalog-TheBioCatalogatEBIYellowBAGI-BioAccessGuidetotheInternetatHoustonUniversitySoftwarelibraryfromGDBCAT-DatabasescatalogatINFOBIOGENMBDL-MolecularBiologyDatabaseListAmosWWWlinkspageNucleicAcidsResearchdatabaseissue第35页，本讲稿共80页Human CEPH-genotypedatabaseCEPHhomepage-aresear
33、chlaboratorywhichconstructsmapsofthehumangenomeGeneMap99-AGeneMapoftheHumanGenome(NCBI)OMIM-OnlineMendelianInheritanceinManGENATLAS-HumangenesatlasGeneClinics-MedicalgeneticsknowledgebaseGDB-HumangenesandgenomicmapsGeneCards-Dbintegratinginformationonhumangenes第36页，本讲稿共80页Human UDB-UnifieddbforHuman
34、genomemappingEnsembl-HumangenomeannotationssiteUCSChumangenomeworkingdraftTIGRHGI-TIGRHumanGeneIndexHumanBACEndsDatabase-Non-redundanthumanBACendsequencesHsUniGene-HumantranscriptsinGenBank(ESTclusters)STACK-SequenceTagAlignmentandConsensusKnowledgebase(DbofconsensushumanESTs)第37页，本讲稿共80页Human Allge
35、nes.org-Humanpredictedgeneindex/catalogGenLink-HumangeneticsresourceGENOTK-HumancDNAdbHUGE-HumanUnidentifiedGene-EncodedlargeproteinscDNA(KIAA.)CGAP-CancerGenomeAnatomyProjectSCDb-Stemcelldb第38页，本讲稿共80页Human HuGeMap-HumangenomegeneticandphysicalmapdataG3-RH-StanfordG3andTNGradiationhybridmapsGB4-RH-
36、Genebridge4(GB4)humanradiationhybridmapsRadiationHybridDatabase-Radiationhybridmapdata第39页，本讲稿共80页 Human chromosome 18Chr1-Humanchromosome1atRockefellerUniversityMirroratEBIChr3-Humanchromosome3dbattheUniversityofTexasHealthScienceCenterChr7-Humanchromosome7dbatOntariosHospitalforSickChildrenChr8SWI
37、SS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome8第40页，本讲稿共80页Human chromosome911Chr9SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome9Chr9-Humanchromosome9dbChr10SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome10GTCChr10data-Humanchromosome10datafromGenomeTherapeuticsCorpor
38、ationChr11SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome1111DB-Humanchromosome11dbatImperialCollege(U.K.)第41页，本讲稿共80页Human chromosome1216Chr12SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome12Chr13-Humanchromosome13dbatColumbiaChr14SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhum
39、anchromosome14Chr15SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome15Chr15UBC-Humanchromosome15WWWpageatUBCChr16SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome16第42页，本讲稿共80页Human chromosome1619 Chr16LANL-Humanchromosome16dbatLosAlamosNationalLaboratoryChr16TIGR-Humanchromosome16
40、dbatTIGRChr17SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome17Chr18SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome18Chr18-Humanchromosome18atBostonChildrensHospitalChr19SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome19第43页，本讲稿共80页Human chromosome2022Chr20SWISS-PROTli
41、st-LinkstoSWISS-PROTentriesfromhumanchromosome20Chr21SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosome21Chr21atRIKEN-Humanchromosome21genomesiteatRIKEN(Japan)Chr21atERI-Humanchromosome21genomicsequencedbfromtheEleanorRooseveltInstituteChr22SWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchr
42、omosome22Chr22atSanger-SangerCenterchromosome22projectChr22atHGC-Humangenomecenterforchromosome22第44页，本讲稿共80页Human chromosomeXYChrXSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeXIXDB-IntegratedXchromosomedbChrYSWISS-PROTlist-LinkstoSWISS-PROTentriesfromhumanchromosomeYDRESH-HumancDNAclon
43、eshomologoustoDrosophilamutantgenes第45页，本讲稿共80页Vertebrates OMIA-OnlineMendelianInheritanceinAnimalsMGI-MouseGenomeInformatics(includesMouseGenomeDatabase(MGD)MirrorsinAustralia|UK|JapanTIGRMGI-TIGRMouseGeneIndexMmUniGene-MousetranscriptsinGenBank(ESTclusters)RatMAP-RatgenomedbTIGRRGI-TIGRRatGeneInde
44、xRnUnigene-RattranscriptsinGenBank(ESTclusters)第46页，本讲稿共80页Vertebrates BovBASE-Bovinegenomedb(inUK)BOVMAP-Bovinegenomedb(inFrance)Ark-Cat-CatgenomedbHorseBASE-HorsegenomedbDGP-DogGenomeProjectPiGBASE-PiggenomedbSheepBASE-Sheepgenomedb(alsoknownasSheepMap)MirrorinUKMIS-MendelianInheritanceinSheepChic
45、kGBASE-Chickengenomedb第47页，本讲稿共80页VertebratesFugu-HGMPResourceCentreFuguProject(Fugurubripes)Medakafish-Mekadafish(Oryziaslatipes)serverArk-Tilapia-TilapiamossambicagenomedbThefishnet-ZebrafishserverFishBase-Globalinformationsystemonfishes第48页，本讲稿共80页Mitochondrion and chloroplast GOBASE-OrganelleGen
46、omeDatabaseMitoDat-MendelianInheritanceandtheMitochondriondb(mitochondrialnucleargenes)MITOMAP-HumanmitochondrialgenomedbMmtDB-MetazoamitochondrialDNAvariantsdbMitBASE-IntegratedmitochondrialDNAdbMitBASE-Pilot-DbofS.cerevisiaenucleargenesinvolvedinmitochondrialbiogenesisHvrBase-PrimatesmtDNAcontrolr
47、egionsequencescompilation第49页，本讲稿共80页Mitochondrion and chloroplastMOUSE-MitochondrialandOtherUsefulSEquences(humanandapesmit.DNAdb)MITOP-Mitochondrialproteins,genesanddiseasesAMmtDB-MetazoanmitochondrialDNAsequences第50页，本讲稿共80页InsectsDrosophilaSWISS-PROTlist-LinkstoDrosophilaSWISS-PROTentriesFlyBase
48、-DrosophilageneticandmoleculardbMirroratEBIFlyView-DrosophilaimagedbGIFTS-GeneInteractionsintheFlyTrans-WorldServerFlyNets-DbofmolecularinteractionsinDrosophilamelanogasterSOS-DGBD-DbofDrosophilaDNAsequencesannotatedwithregulatorybindingsitesMosquitoGenomics第51页，本讲稿共80页InvertebratesWormBase-C.elegan
49、sdbMirroratSangerC.elegansWWWserver-atUniversityofTexasSouthwesternACeDb-CaenorhabditiselegansdbC.elegansMitochondrialDirectory-DataonC.elegansgenesformitochondrialproteinsC.elegansEST-C.elegansESTdbfromJapan(YujiKoharasgroup)C.elegansSWISS-PROTlist-LinkstoC.elegansSWISS-PROTentriesWormPep-C.elegans
50、proteinsdbWormPD-C.elegansproteindb第52页，本讲稿共80页InvertebratesDictysteliumGenomeSequencingprojectatBCMDictyosteliumdiscoideumgenomeprojectatIENADictyDb-DictyosteliumdiscoideumdbDicty_cDB-DictyosteliumdiscoideumcDNAprojectConeshellsWebsiteParasitegenomesdbandresourcesParasitegenomesWWWsitePlasmoDB-P.fa