生物信息學(xué)相關(guān)數(shù)據(jù)庫資源介紹

1、生物信息學(xué)相關(guān)數(shù)據(jù)庫資源介紹l核酸及其相關(guān)數(shù)據(jù)庫（序列數(shù)據(jù)庫、基因組相關(guān)數(shù)據(jù)庫、核酸三維結(jié)構(gòu)數(shù)據(jù)庫、其他）l蛋白質(zhì)相關(guān)數(shù)據(jù)庫（序列數(shù)據(jù)庫、蛋白質(zhì)三維結(jié)構(gòu)數(shù)據(jù)庫、蛋白質(zhì)組數(shù)據(jù)庫（二維凝膠電泳數(shù)據(jù)庫）、信號傳導(dǎo)及蛋白質(zhì)-蛋白質(zhì)相互作用相關(guān)數(shù)據(jù)庫、DNA和蛋白質(zhì)相互作用數(shù)據(jù)庫）l基因或蛋白質(zhì)一些特定數(shù)據(jù)庫l糖類及其相關(guān)數(shù)據(jù)庫l蛋白質(zhì)翻譯后修飾相關(guān)數(shù)據(jù)庫l基因表達(dá)數(shù)據(jù)庫l人類基因突變及疾病相關(guān)數(shù)據(jù)庫l進化相關(guān)數(shù)據(jù)庫及資源專利數(shù)據(jù)庫l資源目錄服務(wù)器或網(wǎng)頁核酸及其相關(guān)數(shù)據(jù)庫（序列數(shù)據(jù)庫、基因組相關(guān)數(shù)據(jù)庫、核酸三維結(jié)構(gòu)數(shù)據(jù)庫、其他）蛋白質(zhì)相關(guān)數(shù)據(jù)庫（序列數(shù)據(jù)庫、蛋白質(zhì)三維結(jié)構(gòu)數(shù)據(jù)庫、蛋白質(zhì)組數(shù)據(jù)庫（二維凝膠

2、電泳數(shù)據(jù)庫）、信號傳導(dǎo)及蛋白質(zhì)-蛋白質(zhì)相互作用相關(guān)數(shù)據(jù)庫、DNA和蛋白質(zhì)相互作用數(shù)據(jù)庫）基因或蛋白質(zhì)一些特定數(shù)據(jù)庫糖類及其相關(guān)數(shù)據(jù)庫蛋白質(zhì)翻譯后修飾相關(guān)數(shù)據(jù)庫基因表達(dá)數(shù)據(jù)庫人類基因突變及疾病相關(guān)數(shù)據(jù)庫進化相關(guān)數(shù)據(jù)庫及資源專利數(shù)據(jù)庫資源目錄服務(wù)器或網(wǎng)頁1）、核酸序列數(shù)據(jù)庫）、核酸序列數(shù)據(jù)庫l BIOSINO 我國的核酸序列公共數(shù)據(jù)庫lEMBL - EMBL Nucleotide sequence database (EBI) lGenBank - GenBank Nucleotide Sequence database (NCBI)lDDBJ - DNA Data Bank of Japan l

3、dbEST - Database of Expressed Sequence Tags （表達(dá)序列標(biāo)簽）(NCBI) ldbSTS - Database of Sequence Tagged Sites （序列標(biāo)簽位點） (NCBI) lGenomeWeb(HGMP) - A catalogue of useful Web sites for Genomics with a set of collections of genome databases lGSDB - Genome Sequence database (NCGR)lGOLD - Genomes On-line dbl一些數(shù)據(jù)庫的

4、直接鏈接lNDB - Nucleic Acid Databank (3D structures) lBNASDB - Nucleic acid structure db from University of Pune lAsDb - Aberrant Splicing db （異常拼接）（異常拼接）lACUTS - Ancient conserved untranslated DNA sequences db lCodon Usage Db - The frequency of codon use in each organism is made searchable through this

5、 World Wide Web site. lEPD - Eukaryotic Promoter db（真核啟動子）（真核啟動子） lHOVERGEN - Homologous Vertebrate Genes db （同源（同源脊椎動物）脊椎動物）lIMGT - ImMunoGeneTics db Mirror at EBI （免疫遺傳學(xué)免疫遺傳學(xué)）lISIS - Intron Sequence and Information System lRDP - Ribosomal db Project lgRNAs db - Guide RNA db lPLACE - Plant cis-acti

6、ng regulatory DNA elements db lPlantCARE - Plant cis-acting regulatory DNA elements db lsRNA db - Small RNA db lssu rRNA - Small ribosomal subunit db llsu rRNA - Large ribosomal subunit db l5S rRNA - 5S ribosomal RNA db ltmRNA Website ltmRDB - tmRNA dB ltRNA - tRNA compilation（編輯）（編輯） from the Unive

7、rsity of Bayreuth luRNADB - uRNA db lRNA editing - RNA editing site lRNAmod db - RNA modification db lTelDB - Multimedia Telomere（端粒） Resource lTRADAT - TRAnscription Databases and Analysis Tools lSubviral RNA db - Small circular RNAs db (viroid and viroid-like) （類病毒）lCre Transgenic Database - Cre t

8、ransgenic mouse lines lTransgenic/Targeted Mutation Database - Information on transgenic animals and targeted mutations 蛋白質(zhì)序列數(shù)據(jù)庫蛋白質(zhì)序列數(shù)據(jù)庫lPIR-international -The Protein Information Resource (protein sequence) （國際蛋白質(zhì)信息中心，（國際蛋白質(zhì)信息中心，NBRF+JIPID+MIPs,PIR1PIR2PIR3PIR4)） lSWISS-PROT - SWISS-PROT annotated（

9、注釋） protein sequence db (SIB+EBI,EBI創(chuàng)建蛋白質(zhì)專家分析系統(tǒng)ExPASy，北京)lMIPS (Munich information center for protein sequence )（德國慕尼黑蛋白質(zhì)序列信息中心德國慕尼黑蛋白質(zhì)序列信息中心） lPROSITE - PROSITE dictionary of protein sites and patterns lInterPro - Integrated Resources of Proteins Domains and Functional Sites lBLOCKS - BLOCKS db lDO

10、MO - Protein domain db (Automatically generated) lPfam - Protein families db (HMM derived) Mirror at Sanger lPRINTS - Protein Motif fingerprint db lProDom - Protein domain db (Automatically generated) lPROTOMAP - An automatic hierarchical（分等級）（分等級） classification of SWISS-PROT proteins lSBASE - SBAS

11、E domain db (Protein domain sequence library) lSMART - Protein signalling and extracellular domain patterns (Simple Modular Architecture Research Tool) lProClass - Protein sequence alignments and curation of protein families lPDB - Protein Data Bank Mirrors in EBI lBioMagResBank Repository（知識）（知識） f

12、or data on proteins, peptides, and nucleic acids from NMR spectroscopy（光譜學(xué)）（光譜學(xué)） lSWISS-MODEL Repository - Automatically generated protein models db lModBase - Db of comparative protein structure models lCATH - UCL BSM structural classification of proteins lSCOP - Structural classification of protei

13、ns Mirror at USA | Israel | Singapore | Australia lMol_R_Us - Molecules R Us, browser for PDB lBMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server lPRESAGE - Collaborative resource for structural genomics lSBASE - SBASE domain db (Protein domain sequence library) lSMAR

14、T - Protein signalling and extracellular（細(xì)胞外）（細(xì)胞外） domain patterns (Simple Modular Architecture Research Tool) lProClass - Protein sequence alignments and curation of protein families lKabat - Kabat db of protein of immunological interest lPMD - Protein Mutant db lWORLD-2DPAGE - A complete index of

15、2D-PAGE db and servers lPhoretix links - Phoretix page of links to 2D gel db lDIP - Db of Interacting Proteins lINTERACT - Protein-Protein interaction db lProNet - Protein-Protein interaction dblCANSITE - Signal Transductions （信號傳導(dǎo)）（信號傳導(dǎo)）WeblSPAD - Signaling pathway db lCSNDB - Cell Signaling Networ

16、ks db lDPInteract - DNA-Proteins interactions dblAAA - AAA family of ATPases server Acetylcholinesterases lALDH - Aldehyde dehydrogenase （醛脫氫酶，l 醛氧化酶）gene superfamily db lAminoacyl-tRNA synthetases in SWISS-PROT - List of aminoacyl-tRNA synthetases in SWISS-PROT lAARSDB - Aminoacyl-tRNA synthetases

17、db lAllergens in SWISS-PROT - Nomenclature and index（命名和索引） of allergens（過敏原） in SWISS-PROT lAMSDb - Antimicrobial sequences db （抗菌）lAntibody resource page - Links to antibody related Web resources （抗體）lAustralian venom and toxin db （澳大利亞蛇毒）lBacillus thuringiensis toxin specificity db（Bt）lTFII - Bas

18、al transcription factors （轉(zhuǎn)錄子）lBlood group antigens in SWISS-PROT （血型抗原）血型抗原）lBCGD - Breast cancer genes db from MBCR （乳癌）lBRENDA - Db of enzyme functional data lEF-hand CaBP - EF-hand calcium-binding proteins db lCAZy - Carbohydrate-Active enZYmes Web site lCBS domain Cystathionine（胱硫醚,丙氨酸丁氨酸硫醚）Bet

19、a Synthase domain WWW page lCD antigens in SWISS-PROT - Nomenclature for surface proteins of human leucocytes (白血球CD) lCD antigens in PROW - Database on information about CD antigens lChaperonin - Information on GroEL and GroES chaperonins lConotoxins - Information on conotoxins from a Web site on c

20、one shellsl。 etc。 l CarbBank - Complex Carbohydrate Structure Database lGlycoSuiteDB - Db of glycan structures lTGN - The Glycoscience Network lFCCA - Forum Carbohydrates Coming of Age lCARBHYD - Carbohydrate information WWW sites lMonosacharide browser - Space filling Fischer projection for monosac

21、charides （單糖）lO-GlycBase - O-glycosylated（ 使(蛋白質(zhì))糖基化）proteins db lPhosphoBase - Phosphorylation （磷酸化作用)sites db lRESID - Db of Amino Acid Modifications lASDB - Protein products and expression patterns of alternatively-spliced genes lAxeldb - Gene expression in Xenopus lBodyMap - Human and mouse gene

22、 expression data lEpoDB - Genes expressed in vertebrate RBC lFlyView - Drosophila development and genetics （果蠅）lGene Expression Database (GXD) - Mouse gene expression and genomics （鼠）lKidney Development Database Kidney（腎） development and gene expressionlMAGEST - Ascidian (Halocynthia roretzi) gene e

23、xpression patterns lMouse Atlas and Gene Expression Database - Spatially-mapped gene expression data lPEDB - Normal and aberrant prostate（正常、異常前列腺）gene expression lTooth Development Database - Gene expression in dental tissue lTRIPLES - TRansposon-Insertion Phenotypes, Localization and Expression in

24、 Saccharomyces（酵母）lHMGD - Human Gene Mutation dbl SVD - Sequence variation db lHGBASE - Human Genic Bi-Allelic Sequences db lThe SNP consortium ldbSNP - Human single nucleotide polymorphism (SNP) db （單核苷酸多態(tài)性數(shù)據(jù)庫）lList of mutation databases from OMIMl List of mutation databases from IMT (Finland) lADB

25、 - Albinism db (Mutations in human genes causing albinism（白化?。? lAlpha-glucosidase - Information about human acid alpha-glucosidase (GSD-II) lAR mutations - Human androgen receptor mutation db lAntithrombin mutation db （抗凝血突變）lAsthma and Allergy gene db （哮喘和過敏）lBIOMDB - Db of mutations causing tetra

26、hydrobiopterin deficiencies （缺乏四氫生物蝶呤缺乏四氫生物蝶呤lBLMbase - Human BLM mutation db (Bloom snydrom)lBTKbase - Human BTK mutation db (X-linked agammaglobulinemia) （血中丙球蛋白貧乏）lCD40Lbase - Human CD40 ligand mutation db lCOL1/3 mutation - Human Type I and III collagen mutation db lCFTR mutation - Human cystic

27、fibrosis mutation db (CFTR) （囊腫性纖維化，屬遺傳性胰腺病囊腫性纖維化，屬遺傳性胰腺病）lEMD db - Human Emerin (EMD) mutation db (Emery-Dreifuss muscular dystrophy) 肌肉萎縮癥肌肉萎縮癥lKMeyeDB - Eye disease genes db lFVII mutation - Human Factor VII mutation db lHAMSTeRS - Human Factor VIII mutation db (Haemophilia A) lHAeMB - Human Fact

28、or IX mutation db (Haemophilia B) 血友病lFBN1 mutation - Human fibrillin 1 mutation db (Marfan syndrome) lG6PD - Human G6PD deficiency resource lGalt mutation - Human galactose-1-phosphate uridylyltransferase mutation db (Galactosemia)lHEXAdb - Human Hexosaminidase A mutation db (Tay-sachs disease) lIL

29、2RGbase - Human IL2RG (Interleukin-2 receptor gamma) mutation db (X-SCID) lL1CAM mutation - Human L1CAM mutation db lLDLR mutation - Human LDLR mutation db (Familial hypercholesterolemia) lLQTSdb - Long QT syndrome db lNCF1base - Human NCF1 mutation db lNCF2base - Human NCF2 mutation db lNeuromuscul

30、ar diseases web site lNCL - Neuronal Ceroid Lipofuscinoses mutation db lOTCase - Human ornithine transcarbamylase (OTCase) website lCytochrome P450 alleles nomenclature lp53 mutation db - University of Tokyo p53 mutation db lGermline p53 mutation db - University of Prague db of germline p53 mutation

31、s lPAHdb - Human phenylalanine hydroxylase (PAH) mutation db lPAX6 mutation - Human PAX6 mutation db lPrion - Prion and prion disease web site lRAG1base - Human RAG1 mutation db lRAG2base - Human RAG2 mutation db lRB1base - Human retinoblastoma-associated protein (RB) mutation db lRetNet - Retinal I

32、nformation Network lRetina International Scientific Newsletter - Information on Retinal genes, proteins and diseases lTSC - TSC (TSC1/TSC2) variation db lTSC2 - Cardiff-Rotterdam Tuberous Sclerosis (TS) db (Tuberin; TSC2) lTGDB - Tumor gene db lVMD2 mutation - Human VMD2 mutation db lvWF mutation -

33、Human von Willebrand factor (vWF) mutation db lWRN - Human WRN mutation db (Warner disease) lWT1 mutation - Human WT1 mutation db lX-ALD mutation - Human ABCD1 mutation db lClusters of Orthologous Groups (COG) - Phylogenetic classification of proteins from 21 complete genomes lXREFdb - Cross-referen

34、cing of model organism genetics with mammalian phenotypes lTreeBASE - Relational db of phylogenetic informationlThe Tree of lifelDPD - DNA Patent db lAg Patents - Agricultural Biotechnology patents from the USDA （農(nóng)業(yè)生物技術(shù)專利）lUSPTO patent db - USA Patent and Trademark （商標(biāo)）Office patent db lEspcenet - P

35、atent information database from the European Patent Office (worldwide coverage) lThe Delphion Intellectual Property Network (IPN) for searching, viewing, and analyzing patent documents. lBioCatalog - The BioCatalog at EBI lYellow BAGI - Bio Access Guide to the Internet at Houston University l lDBCAT

36、 - Databases catalog at INFOBIOGEN lMBDL - Molecular Biology Database List lAmos WWW links page lNucleic Acids Research database issuelCEPH-genotype databaselCEPH home page - a research laboratory which constructs maps of the human genomelGeneMap99 - A Gene Map of the Human Genome (NCBI) lOMIM - Onl

37、ine Mendelian Inheritance in Man lGENATLAS - Human genes atlas lGeneClinics - Medical genetics knowledge base lGDB - Human genes and genomic maps lGeneCards - Db integrating information on human genes lUDB - Unified db for Human genome mapping lEnsembl - Human genome annotations site lUCSC human gen

38、ome working draft lTIGR HGI - TIGR Human Gene Index lHuman BAC Ends Database - Non-redundant human BAC end sequences lHs UniGene - Human transcripts in GenBank (EST clusters) lSTACK - Sequence Tag Alignment and Consensus Knowledgebase (Db of consensus human ESTs) l - Human predicted gene index/catal

39、og lGenLink - Human genetics resource lGENOTK - Human cDNA db lHUGE - Human Unidentified Gene-Encoded large proteins cDNA (KIAA.) lCGAP - Cancer Genome Anatomy Project lSCDb - Stem cell db lHuGeMap - Human genome genetic and physical map data lG3-RH - Stanford G3 and TNG radiation hybrid maps lGB4-R

40、H - Genebridge4 (GB4) human radiation hybrid maps lRadiation Hybrid Database - Radiation hybrid map data lChr1 - Human chromosome 1 at Rockefeller University Mirror at EBI lChr3 - Human chromosome 3 db at the University of Texas Health Science Center lChr7 - Human chromosome 7 db at Ontarios Hospita

41、l for Sick Children lChr8 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 8 lChr9 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 9 lChr9 - Human chromosome 9 db lChr10 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 10 lGTC Chr10 data - Hu

42、man chromosome 10 data from Genome Therapeutics Corporation lChr11 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 11 l11DB - Human chromosome 11 db at Imperial College (U.K.) lChr12 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 12 lChr13 - Human chromosome

43、13 db at Columbia lChr14 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 14 lChr15 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 15 lChr15 UBC - Human chromosome 15 WWW page at UBC lChr16 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 16

44、lChr16 LANL - Human chromosome 16 db at Los Alamos National Laboratory lChr16 TIGR - Human chromosome 16 db at TIGR lChr17 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 17 lChr18 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 18 lChr18 - Human chromosome 18

45、 at Boston Childrens Hospital lChr19 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 19 lChr20 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 20 lChr21 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 21 lChr21 at RIKEN - Human chromosome 2

46、1 genome site at RIKEN (Japan) lChr21 at ERI - Human chromosome 21 genomic sequence db from the Eleanor Roosevelt Institute lChr22 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 22 lChr22 at Sanger - Sanger Center chromosome 22 project lChr22 at HGC - Human genome center for chr

47、omosome 22 lChrX SWISS-PROT list - Links to SWISS-PROT entries from human chromosome X lIXDB - Integrated X chromosome db lChrY SWISS-PROT list - Links to SWISS-PROT entries from human chromosome YlOMIA - Online Mendelian Inheritance in Animals lMGI - Mouse Genome Informatics (includes *Mouse Genome

48、 Database (MGD)Mirrors in Australia | UK | Japan lTIGR MGI - TIGR Mouse* Gene Index lMm UniGene - Mouse transcripts in GenBank (EST clusters) lRatMAP - Rat genome db lTIGR RGI - TIGR Rat Gene Index lRn Unigene - Rat transcripts in GenBank (EST clusters) (以上與老鼠有關(guān)的基因數(shù)據(jù)庫）lBovBASE - Bovine genome db (in

49、 UK) lBOVMAP - Bovine genome db (in France) （牛） lArk-Cat cat genome db (貓）lHorseBASE - Horse genome db （馬）lDGP - Dog Genome Project （狗）lPiGBASE - Pig genome db （豬）lSheepBASE - Sheep genome db (also known as SheepMap) Mirror in UK （羊）lMIS - Mendelian Inheritance in Sheep lChickGBASE - Chicken genome

50、db （雞）lFugu - HGMP Resource Centre Fugu Project (Fugu rubripes) （河豚）lMedakafish - Mekada fish (Oryzias latipes) server lArk-Tilapia - Tilapia （羅非魚）mossambica genome db lThe fish net - Zebrafish server （斑馬魚）lFishBase - Global information system on fishes lGOBASE - Organelle Genome Database lMitoDat -

51、 Mendelian Inheritance and the Mitochondrion db (mitochondrial nuclear genes) lMITOMAP - Human mitochondrial genome db lMmtDB - Metazoa mitochondrial DNA variants db （后生動物）lMitBASE - Integrated mitochondrial DNA db lMitBASE-Pilot - Db of S.cerevisiae nuclear genes involved in mitochondrial biogenesi

52、s lHvrBase - Primates mtDNA control region sequences compilation lMOUSE - Mitochondrial and Other Useful SEquences (human and apes mit. DNA db) lMITOP - Mitochondrial proteins, genes and diseases lAMmtDB - Metazoan mitochondrial DNA sequences lDrosophila SWISS-PROT list - Links to Drosophila SWISS-P

53、ROT entries （果蠅）lFlyBase - Drosophila genetic and molecular db Mirror at EBI lFlyView - Drosophila image db lGIFTS - Gene Interactions in the Fly Trans-World Server lFlyNets - Db of molecular interactions in Drosophila melanogaster lSOS-DGBD - Db of Drosophila DNA sequences annotated with regulatory

54、 binding sites lMosquito Genomics （蚊子）lWormBase - C.elegans db Mirror at Sanger lC.elegans WWW server - at University of Texas Southwestern （線蟲）lACeDb - Caenorhabditis elegans db lC.elegans Mitochondrial Directory - Data on C.elegans genes for mitochondrial proteins lC.elegans EST - C.elegans EST db

55、 from Japan (Yuji Koharas group) lC.elegans SWISS-PROT list - Links to C.elegans SWISS-PROT entries lWormPep - C.elegans proteins db lWormPD - C.elegans protein db lDictystelium Genome Sequencing project at BCM lDictyostelium discoideum genome project at IENA lDictyDb - Dictyostelium discoideum db l

56、Dicty_cDB - Dictyostelium discoideum cDNA project lCone shells Web site lParasite genomes db and resources （寄生蟲）lParasite genomes WWW site lPlasmoDB - P.falciparum genome db lMalaria - WHO - Malaria db (from WHO) lP.falciparum Sanger - P.falciparum genome project at Sanger lPFDB - Plasmodium falcipa

57、rum Genome db l - Plasmodium falciparum Gene Sequence Tag project （ 瘧原蟲）lMAD - Malaria Antigen db lMalaria parasite metabolic pathways lLGN - Leishmania Genome Network （利什曼蟲）lTrypanosoma brucei genome project （錐體蟲）lTrypanosoma cruzi genome project lkDNA - Kinetoplast Minicircle Sequence db lNAL - AG

58、IS - Access to many plant genome databases at the National Agricultural Library lDemeters genomes - Access to many plant genome databases at the USDA-ARS lMendel - Plant gene nomenclature database from CPGN lAtDB - Arabidopsis thaliana genome database lTAIR - The Arabidopsis Information Resource lMA

59、TDB - MIPS Arabidopsis thaliana db lTIGR AtGI - TIGR Arabidopsis thaliana Gene Index lAGR - Arabidopsis Genome Resource lBeanGenes - Beans genome db （豆）lBeanRef - Beans genome db and other resources lChlamyDB - Chlamydomonas reinhardtii genome db （衣藻）lCropNet - Genome mapping in crop plants （農(nóng)作物）lCo

60、ttonDB - Cotton genome db （棉花）lMaizeDb - Maize genome db （玉米）lINRA Maize - INRA Maize genome db lZmDB - Maize genome database lPisum sativum (pea) web site （豌豆）lRGP - Rice Genome Research Program （水稻）lRiceGenes l - Monsanto rice genome site lTIGR OsGI - TIGR Rice Gene Index lTIGR GmGI - TIGR Soybean