生物信息学相关数据库资源介绍.pptx

1、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（核酸及其相关数据库（核酸核酸序列、基因组相关数序列、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（蛋白质蛋白质序列、蛋白质三维结构、蛋序列、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

2、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进化相关数据库及资源专利数据库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n EMBL-EMBL Nucleotide sequence database(EBI)*nGenBank-GenBank Nucleotide Sequence data

3、base(NCBI)*nDDBJ-DNA Data Bank of Japan*nBIOSINO 我国核酸序列公共数据库ndbEST-Database of Expressed Sequence Tags (NCBI)ndbSTS-Database of Sequence Tagged Sites(NCBI)第3页2.基因组及相关数据库 Genomic DatabasesnGenomeWeb(HGMP)-A catalogue of useful Web sites for Genomics with a set of collections of genome databases nGSDB

4、-Genome Sequence database(NCGR)nGOLD-Genomes On-line dbn一些数据库直接链接第4页3.核酸三维结构数据库nNDB-Nucleic Acid Databank(3D structures)nBNASDB-Nucleic acid structure db from University of Pune 第5页4.其它nAsDb-Aberrant Splicing db nACUTS-Ancient conserved untranslated DNA sequences db nCodon Usage Db -The frequency of

5、 codon use in each organism is made searchable through this World Wide Web site.nEPD-Eukaryotic Promoter db nHOVERGEN-Homologous Vertebrate Genes db nIMGT-ImMunoGeneTics db Mirror at EBI nISIS-Intron Sequence and Information System nRDP-Ribosomal db Project ngRNAs db-Guide RNA db nPLACE-Plant cis-ac

6、ting regulatory DNA elements db 第6页其它其它nPlantCARE-Plant cis-acting regulatory DNA elements db nsRNA db-Small RNA db nssu rRNA-Small ribosomal subunit db nlsu rRNA-Large ribosomal subunit db n5S rRNA-5S ribosomal RNA db ntmRNA Website ntmRDB-tmRNA dB ntRNA-tRNA compilation from the University of Bayr

7、euth nuRNADB-uRNA db 第7页其它其它nRNA editing-RNA editing site nRNAmod db-RNA modification db nTelDB-Multimedia Telomere Resource nTRADAT-TRAnscription Databases and Analysis Tools nSubviral RNA db-Small circular RNAs db(viroid and viroid-like)第8页TransgenicsnCre Transgenic Database-Cre transgenic mouse l

8、ines nTransgenic/Targeted Mutation Database-Information on transgenic animals and targeted mutations 第9页二.蛋白质序列和相关数据库nSWISS-PROT-SWISS-PROT annotated protein sequence db nPIR-international-The Protein Information Resource(protein sequence)nMIPS-Martinsried institute for protein sequence and homology

9、 data and yeast genome information 第10页蛋白质及其相关数据库蛋白质及其相关数据库 nPROSITE-PROSITE dictionary of protein sites and patterns nInterPro-Integrated Resources of Proteins Domains and Functional Sites nBLOCKS-BLOCKS db nDOMO-Protein domain db(Automatically generated)nPfam-Protein families db(HMM derived)Mirror

10、 at Sanger nPRINTS-Protein Motif fingerprint db nProDom-Protein domain db(Automatically generated)nPROTOMAP-An automatic hierarchical classification of SWISS-PROT proteins nSBASE-SBASE domain db(Protein domain sequence library)nSMART-Protein signalling and extracellular domain patterns(Simple Modula

11、r Architecture Research Tool)nProClass-Protein sequence alignments and curation of protein families 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-Protein Data Bank Mirrors in EBI nBioMagResBank-Repository for data on proteins,peptides,and nucleic acids from NMR spectroscopy nSWISS-MODEL Repository-Automatical

12、ly generated protein models db nModBase-Db of comparative protein structure models nCATH-UCL BSM structural classification of proteins nSCOP-Structural classification of proteins Mirror at USA|Israel|Singapore|Australia nMol_R_Us-Molecules R Us,browser for PDB nBMM Domain Server-Biomolecular Modelli

13、ng Laboratory(ICRF)protein domain server nPRESAGE-Collaborative resource for structural genomics 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-SBASE domain db(Protein domain sequence library)nSMART-Protein signalling and extracellular domain patterns(Simple Modular Architecture Research Tool)nProClass-Prote

14、in sequence alignments and curation of protein families nKabat-Kabat db of protein of immunological interest nPMD-Protein Mutant db 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-A complete index of 2D-PAGE db and servers nPhoretix links-Phoretix page of links to 2D gel db 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

15、蛋白质相互作用相关数据库用相关数据库nDIP-Db of Interacting Proteins nINTERACT-Protein-Protein interaction db nProNet-Protein-Protein interaction dbnCANSITE-Signal Transductions WebnSPAD-Signaling pathway db nCSNDB-Cell Signaling Networks db 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-Proteins interactions db第16页

16、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-AAA family of ATPases server Acetylcholinesterases nALDH-Aldehyde dehydrogenase gene superfamily db nAminoacyl-tRNA synthetases in SWISS-PROT-List of aminoacyl-tRNA synthetases in SWISS-PROT nAARSDB-Aminoacyl-tRNA synthetases db nAllergens in SWISS-PROT-Nomenclature an

17、d index of allergens in SWISS-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-Antimicrobial sequences db nAntibody resource page-Links to antibody related Web resources nAustralian venom and toxin db nBacillus thuringiensis toxin specificity dbnTFII-Basal transcription factors nBlood group antigens in SWISS-P

18、ROT nBCGD-Breast cancer genes db from MBCR nBRENDA-Db of enzyme functional data 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-hand CaBP-EF-hand calcium-binding proteins db nCAZy-Carbohydrate-Active enZYmes Web site nCBS domain-Cystathionine Beta Synthase domain WWW page nCD antigens in SWISS-PROT-Nomenclature for s

19、urface proteins of human leucocytes(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nCD antigens in PROW-Database on information about CD antigens nChaperonin-Information on GroEL and GroES chaperonins nConotoxins-Information on conotoxins from a Web site on cone shells。etc。第20页糖类相关数据库糖类相关数据库n CarbBank-Complex Carbohy

20、drate Structure Database GlycoSuiteDB-Db of glycan structures nTGN-The Glycoscience Network nFCCA-Forum Carbohydrates Coming of Age nCARBHYD-Carbohydrate information WWW sites nMonosacharide browser-Space filling Fischer projection for monosaccharides 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-gly

21、cosylated proteins db nPhosphoBase-Phosphorylation sites db nRESID-Db of Amino Acid Modifications 第22页基因表示数据库基因表示数据库 nASDB-Protein products and expression patterns of alternatively-spliced genes nAxeldb-Gene expression in Xenopus nBodyMap-Human and mouse gene expression data nEpoDB-Genes expressed i

22、n vertebrate RBC nFlyView-Drosophila development and genetics nGene Expression Database(GXD)-Mouse gene expression and genomics nKidney Development Database-Kidney development and gene expression第23页基因表示数据库基因表示数据库 nMAGEST-Ascidian(Halocynthia roretzi)gene expression patterns nMouse Atlas and Gene Ex

23、pression Database-Spatially-mapped gene expression data nPEDB-Normal and aberrant prostate gene expression nTooth Development Database-Gene expression in dental tissue nTRIPLES-TRansposon-Insertion Phenotypes,Localization and Expression in Saccharomyces 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-Human Ge

24、ne Mutation db SVD-Sequence variation db nHGBASE-Human Genic Bi-Allelic Sequences db nThe SNP consortium ndbSNP-Human single nucleotide polymorphism(SNP)db nList of mutation databases from OMIM List of mutation databases from IMT(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-Albinism db(Mutations in

25、human genes causing albinism)Alpha-glucosidase-Information about human acid alpha-glucosidase(GSD-II)nAR mutations-Human androgen receptor mutation db nAntithrombin mutation db nAsthma and Allergy gene db nBIOMDB-Db of mutations causing tetrahydrobiopterin deficiencies nBLMbase-Human BLM mutation db

26、(Bloom snydrom)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-Human BTK mutation db(X-linked agammaglobulinemia)nCD40Lbase-Human CD40 ligand mutation db nCOL1/3 mutation-Human Type I and III collagen mutation db nCFTR mutation-Human cystic fibrosis mutation db(CFTR)nEMD db-Human Emerin(EMD)mutation db(Eme

27、ry-Dreifuss muscular dystrophy)nKMeyeDB-Eye disease genes db 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nFVII mutation-Human Factor VII mutation db nHAMSTeRS-Human Factor VIII mutation db(Haemophilia A)nHAeMB-Human Factor IX mutation db(Haemophilia B)nFBN1 mutation-Human fibrillin 1 mutation db(Marfan syndrome

28、)nG6PD-Human G6PD deficiency resource nGalt mutation-Human galactose-1-phosphate uridylyltransferase mutation db(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-Human Hexosaminidase A mutation db(Tay-sachs disease)nIL2RGbase-Human IL2RG(Interleukin-2 receptor gamma)mutation db(X-SCID)nL1CAM mut

29、ation-Human L1CAM mutation db nLDLR mutation-Human LDLR mutation db(Familial hypercholesterolemia)nLQTSdb-Long QT syndrome db nNCF1base-Human NCF1 mutation db nNCF2base-Human NCF2 mutation db 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nNeuromuscular diseases web site nNCL-Neuronal Ceroid Lipofuscinoses mutatio

30、n db nOTCase-Human ornithine transcarbamylase(OTCase)website nCytochrome P450 alleles nomenclature np53 mutation db-University of Tokyo p53 mutation db nGermline p53 mutation db-University of Prague db of germline p53 mutations nPAHdb-Human phenylalanine hydroxylase(PAH)mutation db 第30页人类基因突变及疾病相关数据

31、库人类基因突变及疾病相关数据库nPAX6 mutation-Human PAX6 mutation db nPrion-Prion and prion disease web site nRAG1base-Human RAG1 mutation db nRAG2base-Human RAG2 mutation db nRB1base-Human retinoblastoma-associated protein(RB)mutation db nRetNet-Retinal Information Network nRetina International Scientific Newslett

32、er-Information on Retinal genes,proteins and diseases 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)variation db nTSC2-Cardiff-Rotterdam Tuberous Sclerosis(TS)db(Tuberin;TSC2)nTGDB-Tumor gene db nVMD2 mutation-Human VMD2 mutation db nvWF mutation-Human von Willebrand factor(vWF)mutation db nWRN

33、-Human WRN mutation db(Warner disease)nWT1 mutation-Human WT1 mutation db nX-ALD mutation-Human ABCD1 mutation db 第32页进化相关数据库及资源进化相关数据库及资源 nClusters of Orthologous Groups(COG)-Phylogenetic classification of proteins from 21 complete genomes nXREFdb-Cross-referencing of model organism genetics with m

34、ammalian phenotypes nTreeBASE-Relational db of phylogenetic informationnThe Tree of life-Collection of WWW pages on phylogeny and biodiversity of organisms 第33页专利数据库专利数据库 nDPD-DNA Patent db nAg Patents-Agricultural Biotechnology patents from the USDA nUSPTO patent db-USA Patent and Trademark Office

35、patent db nEspcenet-Patent information database from the European Patent Office(worldwide coverage)nThe Delphion Intellectual Property Network(IPN)for searching,viewing,and analyzing patent documents.第34页资源目录服务器或网页资源目录服务器或网页nBioCatalog-The BioCatalog at EBI nYellow BAGI-Bio Access Guide to the Inter

36、net at Houston University nSoftware library from G nDBCAT-Databases catalog at INFOBIOGEN nMBDL-Molecular Biology Database List nAmos WWW links page nNucleic Acids Research database issue第35页Human nCEPH-genotype databasenCEPH home page-a research laboratory which constructs maps of the human genomen

37、GeneMap99-A Gene Map of the Human Genome(NCBI)nOMIM-Online Mendelian Inheritance in Man nGENATLAS-Human genes atlas nGeneClinics-Medical genetics knowledge base nGDB-Human genes and genomic maps nGeneCards-Db integrating information on human genes 第36页Human nUDB-Unified db for Human genome mapping n

38、Ensembl-Human genome annotations site nUCSC human genome working draft nTIGR HGI-TIGR Human Gene Index nHuman BAC Ends Database-Non-redundant human BAC end sequences nHs UniGene-Human transcripts in GenBank(EST clusters)nSTACK-Sequence Tag Alignment and Consensus Knowledgebase(Db of consensus human

39、ESTs)第37页Human nAllgenes.org-Human predicted gene index/catalog nGenLink-Human genetics resource nGENOTK-Human cDNA db nHUGE-Human Unidentified Gene-Encoded large proteins cDNA(KIAA.)nCGAP-Cancer Genome Anatomy Project nSCDb-Stem cell db 第38页Human nHuGeMap-Human genome genetic and physical map data

40、nG3-RH-Stanford G3 and TNG radiation hybrid maps nGB4-RH-Genebridge4(GB4)human radiation hybrid maps nRadiation Hybrid Database-Radiation hybrid map data 第39页 Human chromosome 18nChr1-Human chromosome 1 at Rockefeller University Mirror at EBI nChr3-Human chromosome 3 db at the University of Texas He

41、alth Science Center nChr7-Human chromosome 7 db at Ontarios Hospital for Sick Children nChr8 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 8 第40页Human chromosome911nChr9 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 9 nChr9-Human chromosome 9 db nChr10 SWISS-P

42、ROT list-Links to SWISS-PROT entries from human chromosome 10 nGTC Chr10 data-Human chromosome 10 data from Genome Therapeutics Corporation nChr11 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 11 n11DB-Human chromosome 11 db at Imperial College(U.K.)第41页Human chromosome1216nChr12

43、 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 12 nChr13-Human chromosome 13 db at Columbia nChr14 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 14 nChr15 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 15 nChr15 UBC-Human chromosome 15 WWW p

44、age at UBC nChr16 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 16第42页Human chromosome1619 nChr16 LANL-Human chromosome 16 db at Los Alamos National Laboratory nChr16 TIGR-Human chromosome 16 db at TIGR nChr17 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 17 n

45、Chr18 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 18 nChr18-Human chromosome 18 at Boston Childrens Hospital nChr19 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 19 第43页Human chromosome2022nChr20 SWISS-PROT list-Links to SWISS-PROT entries from human chromos

46、ome 20 nChr21 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 21 nChr21 at RIKEN-Human chromosome 21 genome site at RIKEN(Japan)nChr21 at ERI-Human chromosome 21 genomic sequence db from the Eleanor Roosevelt Institute nChr22 SWISS-PROT list-Links to SWISS-PROT entries from human c

47、hromosome 22 nChr22 at Sanger-Sanger Center chromosome 22 project nChr22 at HGC-Human genome center for chromosome 22 第44页Human chromosomeXYnChrX SWISS-PROT list-Links to SWISS-PROT entries from human chromosome X nIXDB-Integrated X chromosome db nChrY SWISS-PROT list-Links to SWISS-PROT entries fro

48、m human chromosome Y nnDRESH-Human cDNA clones homologous to Drosophila mutant genes第45页Vertebrates nOMIA-Online Mendelian Inheritance in Animals nMGI-Mouse Genome Informatics(includes Mouse Genome Database(MGD)Mirrors in Australia|UK|Japan nTIGR MGI-TIGR Mouse Gene Index nMm UniGene-Mouse transcrip

49、ts in GenBank(EST clusters)nRatMAP-Rat genome db nTIGR RGI-TIGR Rat Gene Index nRn Unigene-Rat transcripts in GenBank(EST clusters)第46页Vertebrates nBovBASE-Bovine genome db(in UK)nBOVMAP-Bovine genome db(in France)nArk-Cat-Cat genome db nHorseBASE-Horse genome db nDGP-Dog Genome Project nPiGBASE-Pig

50、 genome db nSheepBASE-Sheep genome db(also known as SheepMap)Mirror in UK nMIS-Mendelian Inheritance in Sheep nChickGBASE-Chicken genome db 第47页VertebratesnFugu-HGMP Resource Centre Fugu Project(Fugu rubripes)nMedakafish-Mekada fish(Oryzias latipes)server nArk-Tilapia-Tilapia mossambica genome db nT