生物信息学相关数据库资源介绍

1、 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、其他）据库、核酸三维结构、其他）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

2、译后修饰相关数据库蛋白质翻译后修饰相关数据库6.基因表达数据库基因表达数据库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 database (NCBI) * nDDBJ - DNA Data Bank of Japan * nBIOSINO

3、我国的核酸序列公共数据库ndbEST - Database of Expressed Sequence Tags (NCBI) ndbSTS - Database of Sequence Tagged Sites (NCBI) 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 - Genome Sequence database (NCGR)nGOLD -

4、Genomes On-line dbn一些数据库的直接链接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 4.其他nAsDb - Aberrant Splicing db nACUTS - Ancient conserved untranslated DNA sequences db nCodon Usage Db - The frequency of codon use in each organism is

5、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-acting regulatory

6、DNA elements db 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 Bayreuth

7、nuRNADB - uRNA db 其他其他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) TransgenicsnCre Transgenic Database - Cre transgenic mo

8、use lines nTransgenic/Targeted Mutation Database - Information on transgenic animals and targeted mutations 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 a

9、nd homology data and yeast genome information 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

10、 (HMM derived) Mirror 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 extracel

11、lular domain patterns (Simple Modular Architecture Research Tool) nProClass - Protein sequence alignments and curation of protein families .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 spectro

12、scopy nSWISS-MODEL Repository - Automatically 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 U

13、s, browser for PDB nBMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server nPRESAGE - Collaborative resource for structural genomics 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

14、patterns (Simple Modular Architecture Research Tool) nProClass - Protein sequence alignments and curation of protein families nKabat - Kabat db of protein of immunological interest nPMD - Protein Mutant db 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 l

15、inks - Phoretix page of links to 2D gel db 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 - Db of Interacting Proteins nINTERACT - Protein-Protein interaction db nProNet - Protein-Protein interaction dbnCANSITE - Signal Transductions WebnSPAD - Signaling pathway db nCSNDB - Cell Signaling Network

16、s db 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五、特定基因或蛋白质的数据库五、特定基因或蛋白质的数据库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

17、-PROT nAARSDB - Aminoacyl-tRNA synthetases db nAllergens in SWISS-PROT - Nomenclature and index of allergens in SWISS-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nAMSDb - Antimicrobial sequences db nAntibody resource page - Links to antibody related Web resources nAustralian venom and toxin db nBacillus thuringien

18、sis toxin specificity dbnTFII - Basal transcription factors nBlood group antigens in SWISS-PROT nBCGD - Breast cancer genes db from MBCR nBRENDA - Db of enzyme functional data 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-hand CaBP - EF-hand calcium-binding proteins db nCAZy - Carbohydrate-Active enZYmes Web site nCB

19、S domain - Cystathionine Beta Synthase domain WWW page nCD antigens in SWISS-PROT - Nomenclature for surface proteins of human leucocytes (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nCD antigens in PROW - Database on information about CD antigens nChaperonin - Information on GroEL and GroES chaperonins nConotoxins

20、 - Information on conotoxins from a Web site on cone shells。 etc。 糖类相关数据库糖类相关数据库n CarbBank - Complex Carbohydrate Structure Database GlycoSuiteDB - Db of glycan structures nTGN - The Glycoscience Network nFCCA - Forum Carbohydrates Coming of Age nCARBHYD - Carbohydrate information WWW sites nMonosac

21、haride browser - Space filling Fischer projection for monosaccharides 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-glycosylated proteins db nPhosphoBase - Phosphorylation sites db nRESID - Db of Amino Acid Modifications 基因表达数据库基因表达数据库 nASDB - Protein products and expression patterns of alternatively-s

22、pliced genes nAxeldb - Gene expression in Xenopus nBodyMap - Human and mouse gene expression data nEpoDB - Genes expressed in vertebrate RBC nFlyView - Drosophila development and genetics nGene Expression Database (GXD) - Mouse gene expression and genomics nKidney Development Database - Kidney devel

23、opment and gene expression基因表达数据库基因表达数据库 nMAGEST - Ascidian (Halocynthia roretzi) gene expression patterns nMouse Atlas and Gene Expression Database - Spatially-mapped gene expression data nPEDB - Normal and aberrant prostate gene expression nTooth Development Database - Gene expression in dental ti

24、ssue nTRIPLES - TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces 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 Gene Mutation db SVD - Sequence variation db nHGBASE - Human Genic Bi-Allelic Sequences db nThe SNP consortium ndbSNP - Human single nucleotide polymorphism (SNP) d

25、b nList of mutation databases from OMIM List of mutation databases from IMT (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 - Albinism db (Mutations in human genes causing albinism) Alpha-glucosidase - Information about human acid alpha-glucosidase (GSD-II) nAR mutations - Human androgen receptor mutatio

26、n db nAntithrombin mutation db nAsthma and Allergy gene db nBIOMDB - Db of mutations causing tetrahydrobiopterin deficiencies nBLMbase - Human BLM mutation db (Bloom snydrom)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 muta

27、tion 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 (Emery-Dreifuss muscular dystrophy) nKMeyeDB - Eye disease genes db 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 mu

28、tation 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) nG6PD - Human G6PD deficiency resource nGalt mutation - Human galactose-1-phosphate uridylyltransferase mutation d

29、b (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 - Human Hexosaminidase A mutation db (Tay-sachs disease) nIL2RGbase - Human IL2RG (Interleukin-2 receptor gamma) mutation db (X-SCID) nL1CAM mutation - Human L1CAM mutation db nLDLR mutation - Human LDLR mutation db (Familial hypercholesterolemia)

30、nLQTSdb - Long QT syndrome db nNCF1base - Human NCF1 mutation db nNCF2base - Human NCF2 mutation db 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 mutation db nOTCase - Human ornithine transcarbamylase (OTCase) website nCytochrome P450 alleles nome

31、nclature 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 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nPAX6 mutation - Human PAX6 mutation db nPrion - Prion and prion diseas

32、e 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 Newsletter - Information on Retinal genes, proteins and diseases 人类基因突变及疾病相关数据库人

33、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 - Human WRN mutation db (Warner disease) nWT1 mutatio

34、n - Human WT1 mutation db nX-ALD mutation - Human ABCD1 mutation db 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 mammalian phenotypes nTreeBASE - Relational db

35、 of phylogenetic informationnThe Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms 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 patent db nEspcenet - Patent informatio

36、n database from the European Patent Office (worldwide coverage) nThe Delphion Intellectual Property Network (IPN) for searching, viewing, and analyzing patent documents. 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 Internet at Houston University nSof

37、tware library from G nDBCAT - Databases catalog at INFOBIOGEN nMBDL - Molecular Biology Database List nAmos WWW links page nNucleic Acids Research database issueHuman nCEPH-genotype databasenCEPH home page - a research laboratory which constructs maps of the human genomenGeneMap99 - A Gene Map of th

38、e 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 Human nUDB - Unified db for Human genome mapping nEnsembl - Human

39、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 EST

40、s) Human nA - 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 Human nHuGeMap - Human genome genetic and physical map

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

42、y of Texas Health 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 Human chromosome911nChr9 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 9 nChr9 - Human chromosome 9

43、db nChr10 SWISS-PROT 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.) Hum

44、an chromosome1216nChr12 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 nChr1

45、5 UBC - Human chromosome 15 WWW page at UBC nChr16 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 16Human 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-PR

46、OT entries from human chromosome 17 nChr18 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 Human chromosome2022nChr20 SWISS-PROT list - Links

47、 to SWISS-PROT entries from human chromosome 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-P

48、ROT list - Links to SWISS-PROT entries from human chromosome 22 nChr22 at Sanger - Sanger Center chromosome 22 project nChr22 at HGC - Human genome center for chromosome 22 Human chromosomeXYnChrX SWISS-PROT list - Links to SWISS-PROT entries from human chromosome X nIXDB - Integrated X chromosome d

49、b nChrY SWISS-PROT list - Links to SWISS-PROT entries from human chromosome Y nnDRESH - Human cDNA clones homologous to Drosophila mutant genesVertebrates nOMIA - Online Mendelian Inheritance in Animals nMGI - Mouse Genome Informatics (includes Mouse Genome Database (MGD)Mirrors in Australia | UK |

50、Japan nTIGR MGI - TIGR Mouse Gene Index nMm UniGene - Mouse transcripts in GenBank (EST clusters) nRatMAP - Rat genome db nTIGR RGI - TIGR Rat Gene Index nRn Unigene - Rat transcripts in GenBank (EST clusters) Vertebrates nBovBASE - Bovine genome db (in UK) nBOVMAP - Bovine genome db (in France) nAr

51、k-Cat - Cat genome db nHorseBASE - Horse genome db nDGP - Dog Genome Project nPiGBASE - Pig genome db nSheepBASE - Sheep genome db (also known as SheepMap) Mirror in UK nMIS - Mendelian Inheritance in Sheep nChickGBASE - Chicken genome db VertebratesnFugu - HGMP Resource Centre Fugu Project (Fugu ru

52、bripes) nMedakafish - Mekada fish (Oryzias latipes) server nArk-Tilapia - Tilapia mossambica genome db nThe fish net - Zebrafish server nFishBase - Global information system on fishes Mitochondrion and chloroplast nGOBASE - Organelle Genome Database nMitoDat - Mendelian Inheritance and the Mitochond

53、rion db (mitochondrial nuclear genes) nMITOMAP - Human mitochondrial genome db nMmtDB - Metazoa mitochondrial DNA variants db nMitBASE - Integrated mitochondrial DNA db nMitBASE-Pilot - Db of S.cerevisiae nuclear genes involved in mitochondrial biogenesis nHvrBase - Primates mtDNA control region seq

54、uences compilationMitochondrion and chloroplastnMOUSE - Mitochondrial and Other Useful SEquences (human and apes mit. DNA db) nMITOP - Mitochondrial proteins, genes and diseases nAMmtDB - Metazoan mitochondrial DNA sequences InsectsnDrosophila SWISS-PROT list - Links to Drosophila SWISS-PROT entries

55、 nFlyBase - Drosophila genetic and molecular db Mirror at EBI nFlyView - Drosophila image db nGIFTS - Gene Interactions in the Fly Trans-World Server nFlyNets - Db of molecular interactions in Drosophila melanogaster nSOS-DGBD - Db of Drosophila DNA sequences annotated with regulatory binding sites

56、nMosquito Genomics InvertebratesnWormBase - C.elegans db Mirror at Sanger nC.elegans WWW server - at University of Texas Southwestern nACeDb - Caenorhabditis elegans db nC.elegans Mitochondrial Directory - Data on C.elegans genes for mitochondrial proteins nC.elegans EST - C.elegans EST db from Japa

57、n (Yuji Koharas group) nC.elegans SWISS-PROT list - Links to C.elegans SWISS-PROT entries nWormPep - C.elegans proteins db nWormPD - C.elegans protein db InvertebratesnDictystelium Genome Sequencing project at BCM nDictyostelium discoideum genome project at IENA nDictyDb - Dictyostelium discoideum d

58、b nDicty_cDB - Dictyostelium discoideum cDNA project nCone shells Web site nParasite genomes db and resources nParasite genomes WWW site nPlasmoDB - P.falciparum genome db InvertebratesnMalaria - WHO - Malaria db (from WHO) （疟疾nue）nP.falciparum Sanger - P.falciparum genome project at Sanger nPFDB -

59、Plasmodium falciparum Genome db （疟原虫）nP.falciparum - Plasmodium falciparum Gene Sequence Tag project InvertebratesnMAD - Malaria Antigen db nMalaria parasite metabolic pathways nLGN - Leishmania Genome Network nTrypanosoma brucei genome project nTrypanosoma cruzi genome project nkDNA - Kinetoplast M

60、inicircle Sequence db PlantsnNAL - AGIS - Access to many plant genome databases at the National Agricultural Library nDemeters genomes - Access to many plant genome databases at the USDA-ARS nMendel - Plant gene nomenclature database from CPGN nAtDB - Arabidopsis thaliana genome database nTAIR - The