很好—生物信息相关数据库资源介绍ppt课件.ppt

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1、生物信息学数据库资源大全,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,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（

2、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,核酸及其相关数据库,1）、核酸序列数据库 BIOSINO 我国的核酸序列公共数据库EMBL - EMBL Nucleotide sequence database (EBI) GenBank - GenBank Nucleotide Sequence database (NCBI)DDBJ - DNA Data Bank of Japan

3、 dbEST - Database of Expressed Sequence Tags （表达序列标签）(NCBI) dbSTS - Database of Sequence Tagged Sites （序列标签位点） (NCBI),2）.基因组及相关数据库 Genomic Databases,GenomeWeb(HGMP) - A catalogue of useful Web sites for Genomics with a set of collections of genome databasesGSDB - Genome Sequence database (NCGR)GOLD

4、- Genomes On-line db一些数据库的直接链接,3）.核酸三维结构数据库,NDB - Nucleic Acid Databank (3D structures) BNASDB - Nucleic acid structure db from University of Pune,4）.其他,AsDb - Aberrant Splicing db （异常拼接）ACUTS - Ancient conserved untranslated DNA sequences db Codon Usage Db - The frequency of codon use in each organ

5、ism is made searchable through this World Wide Web site. EPD - Eukaryotic Promoter db（真核启动子） HOVERGEN - Homologous Vertebrate Genes db （同源脊椎动物）IMGT - ImMunoGeneTics db Mirror at EBI （免疫遗传学）ISIS - Intron Sequence and Information System RDP - Ribosomal db Project gRNAs db - Guide RNA db PLACE - Plant

6、cis-acting regulatory DNA elements db,5）其它核酸数据库,PlantCARE - Plant cis-acting regulatory DNA elements db sRNA db - Small RNA db ssu rRNA - Small ribosomal subunit db lsu rRNA - Large ribosomal subunit db 5S rRNA - 5S ribosomal RNA db tmRNA Website tmRDB - tmRNA dB tRNA - tRNA compilation（编辑） from the

7、 University of Bayreuth uRNADB - uRNA db,5）其他核酸数据库,RNA editing - RNA editing site RNAmod db - RNA modification db TelDB - Multimedia Telomere（端粒） Resource TRADAT - TRAnscription Databases and Analysis Tools Subviral RNA db - Small circular RNAs db (viroid and viroid-like) （类病毒）,5）Transgenics（转基因）,Cr

8、e Transgenic Database - Cre transgenic mouse lines Transgenic/Targeted Mutation Database - Information on transgenic animals and targeted mutations,2.蛋白质序列和相关数据库,蛋白质序列数据库PIR-international -The Protein Information Resource (protein sequence) （国际蛋白质信息中心，NBRF+JIPID+MIPs,PIR1PIR2PIR3PIR4)） SWISS-PROT -

9、SWISS-PROT annotated（注释） protein sequence db (SIB+EBI,EBI创建蛋白质专家分析系统ExPASy，北京)MIPS (Munich information center for protein sequence )（德国慕尼黑蛋白质序列信息中心）,蛋白质相关数据库,PROSITE - PROSITE dictionary of protein sites and patterns InterPro - Integrated Resources of Proteins Domains and Functional Sites BLOCKS - B

10、LOCKS db DOMO - Protein domain db (Automatically generated) Pfam - Protein families db (HMM derived) Mirror at Sanger PRINTS - Protein Motif fingerprint db ProDom - Protein domain db (Automatically generated) PROTOMAP - An automatic hierarchical（分等级） classification of SWISS-PROT proteins SBASE - SBA

11、SE domain db (Protein domain sequence library) SMART - Protein signalling and extracellular domain patterns (Simple Modular Architecture Research Tool) ProClass - Protein sequence alignments and curation of protein families,蛋白质三维结构和相关数据库,PDB - Protein Data Bank Mirrors in EBI BioMagResBank Repositor

12、y（知识） for data on proteins, peptides, and nucleic acids from NMR spectroscopy（光谱学） SWISS-MODEL Repository - Automatically generated protein models db ModBase - Db of comparative protein structure models CATH - UCL BSM structural classification of proteins SCOP - Structural classification of proteins

13、 Mirror at USA | Israel | Singapore | Australia Mol_R_Us - Molecules R Us, browser for PDB BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server PRESAGE - Collaborative resource for structural genomics,蛋白质三维结构和相关数据库,SBASE - SBASE domain db (Protein domain sequence librar

14、y) SMART - Protein signalling and extracellular（细胞外） domain patterns (Simple Modular Architecture Research Tool) ProClass - Protein sequence alignments and curation of protein families Kabat - Kabat db of protein of immunological interest PMD - Protein Mutant db,蛋白质二维凝胶电泳数据库,WORLD-2DPAGE - A complet

15、e index of 2D-PAGE db and servers Phoretix links - Phoretix page of links to 2D gel db,3、信号传导及蛋白质-蛋白质相互作用相关数据库,DIP - Db of Interacting Proteins INTERACT - Protein-Protein interaction db ProNet - Protein-Protein interaction dbCANSITE - Signal Transductions （信号传导）WebSPAD - Signaling pathway db CSNDB -

16、 Cell Signaling Networks db,DNA和蛋白质相互作用数据库,DPInteract - DNA-Proteins interactions db,特定基因或蛋白质的数据库,AAA - AAA family of ATPases server Acetylcholinesterases ALDH - Aldehyde dehydrogenase （醛脱氢酶， 醛氧化酶）gene superfamily db Aminoacyl-tRNA synthetases in SWISS-PROT - List of aminoacyl-tRNA synthetases in SW

17、ISS-PROT AARSDB - Aminoacyl-tRNA synthetases db Allergens in SWISS-PROT - Nomenclature and index（命名和索引） of allergens（过敏原） in SWISS-PROT,特定基因或蛋白质的数据库,AMSDb - Antimicrobial sequences db （抗菌）Antibody resource page - Links to antibody related Web resources （抗体）Australian venom and toxin db （澳大利亚蛇毒）Bacil

18、lus thuringiensis toxin specificity db（Bt）TFII - Basal transcription factors （转录子）Blood group antigens in SWISS-PROT （血型抗原）BCGD - Breast cancer genes db from MBCR （乳癌）BRENDA - Db of enzyme functional data,特定基因或蛋白质的数据库,EF-hand CaBP - EF-hand calcium-binding proteins db CAZy - Carbohydrate-Active enZY

19、mes Web site CBS domain Cystathionine（胱硫醚,丙氨酸丁氨酸硫醚）Beta Synthase domain WWW page CD antigens in SWISS-PROT - Nomenclature for surface proteins of human leucocytes (白血球CD),特定基因或蛋白质的数据库,CD antigens in PROW - Database on information about CD antigens Chaperonin - Information on GroEL and GroES chaperon

20、ins Conotoxins - Information on conotoxins from a Web site on cone shells。 etc。,4、糖类相关数据库,CarbBank - Complex Carbohydrate Structure Database GlycoSuiteDB - Db of glycan structures TGN - The Glycoscience Network FCCA - Forum Carbohydrates Coming of Age CARBHYD - Carbohydrate information WWW sites Mon

21、osacharide browser - Space filling Fischer projection for monosaccharides （单糖）,5、蛋白质翻译后修饰相关数据库,O-GlycBase - O-glycosylated（ 使(蛋白质)糖基化）proteins db PhosphoBase - Phosphorylation （磷酸化作用)sites db RESID - Db of Amino Acid Modifications,6、基因表达数据库,ASDB - Protein products and expression patterns of alternat

22、ively-spliced genes Axeldb - Gene expression in Xenopus BodyMap - Human and mouse gene expression data EpoDB - Genes expressed in vertebrate RBC FlyView - Drosophila development and genetics （果蝇）Gene Expression Database (GXD) - Mouse gene expression and genomics （鼠）Kidney Development Database Kidney

23、（肾） development and gene expression,6、基因表达数据库,MAGEST - Ascidian (Halocynthia roretzi) gene expression patterns Mouse Atlas and Gene Expression Database - Spatially-mapped gene expression data PEDB - Normal and aberrant prostate（正常、异常前列腺）gene expression Tooth Development Database - Gene expression in

24、 dental tissue TRIPLES - TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces（酵母）,7、人类基因突变及疾病相关数据库,HMGD - Human Gene Mutation db SVD - Sequence variation db HGBASE - Human Genic Bi-Allelic Sequences db The SNP consortium dbSNP - Human single nucleotide polymorphism (SNP) db

25、（单核苷酸多态性数据库）List 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,ADB - Albinism db (Mutations in human genes causing albinism（白化病）) Alpha-glucosidase - Information about human acid alpha-glucosidase (GSD-II) AR mutations - Human androgen receptor mutation

26、 db Antithrombin mutation db （抗凝血突变）Asthma and Allergy gene db （哮喘和过敏）BIOMDB - Db of mutations causing tetrahydrobiopterin deficiencies （缺乏四氢生物蝶呤BLMbase - Human BLM mutation db (Bloom snydrom),7、人类基因突变及疾病相关数据库,BTKbase - Human BTK mutation db (X-linked agammaglobulinemia) （血中丙球蛋白贫乏）CD40Lbase - Human

27、CD40 ligand mutation db COL1/3 mutation - Human Type I and III collagen mutation db CFTR mutation - Human cystic fibrosis mutation db (CFTR) （囊肿性纤维化，属遗传性胰腺病）EMD db - Human Emerin (EMD) mutation db (Emery-Dreifuss muscular dystrophy) 肌肉萎缩症KMeyeDB - Eye disease genes db,人类基因突变及疾病相关数据库,FVII mutation -

28、Human Factor VII mutation db HAMSTeRS - Human Factor VIII mutation db (Haemophilia A) HAeMB - Human Factor IX mutation db (Haemophilia B) 血友病FBN1 mutation - Human fibrillin 1 mutation db (Marfan syndrome) G6PD - Human G6PD deficiency resource Galt mutation - Human galactose-1-phosphate uridylyltrans

29、ferase mutation db (Galactosemia),人类基因突变及疾病相关数据库,HEXAdb - Human Hexosaminidase A mutation db (Tay-sachs disease) IL2RGbase - Human IL2RG (Interleukin-2 receptor gamma) mutation db (X-SCID) L1CAM mutation - Human L1CAM mutation db LDLR mutation - Human LDLR mutation db (Familial hypercholesterolemia)

30、 LQTSdb - Long QT syndrome db NCF1base - Human NCF1 mutation db NCF2base - Human NCF2 mutation db,人类基因突变及疾病相关数据库,Neuromuscular diseases web site NCL - Neuronal Ceroid Lipofuscinoses mutation db OTCase - Human ornithine transcarbamylase (OTCase) website Cytochrome P450 alleles nomenclature p53 mutati

31、on db - University of Tokyo p53 mutation db Germline p53 mutation db - University of Prague db of germline p53 mutations PAHdb - Human phenylalanine hydroxylase (PAH) mutation db,人类基因突变及疾病相关数据库,PAX6 mutation - Human PAX6 mutation db Prion - Prion and prion disease web site RAG1base - Human RAG1 muta

32、tion db RAG2base - Human RAG2 mutation db RB1base - Human retinoblastoma-associated protein (RB) mutation db RetNet - Retinal Information Network Retina International Scientific Newsletter - Information on Retinal genes, proteins and diseases,人类基因突变及疾病相关数据库,TSC - TSC (TSC1/TSC2) variation db TSC2 -

33、Cardiff-Rotterdam Tuberous Sclerosis (TS) db (Tuberin; TSC2) TGDB - Tumor gene db VMD2 mutation - Human VMD2 mutation db vWF mutation - Human von Willebrand factor (vWF) mutation db WRN - Human WRN mutation db (Warner disease) WT1 mutation - Human WT1 mutation db X-ALD mutation - Human ABCD1 mutatio

34、n db,8、进化相关数据库及资源,Clusters of Orthologous Groups (COG) - Phylogenetic classification of proteins from 21 complete genomes XREFdb - Cross-referencing of model organism genetics with mammalian phenotypes TreeBASE - Relational db of phylogenetic informationThe Tree of life - Collection of WWW pages on

35、phylogeny and biodiversity of organisms http:/phylogeny.arizona.edu/tree/,8、专利数据库,DPD - DNA Patent db Ag Patents - Agricultural Biotechnology patents from the USDA （农业生物技术专利）USPTO patent db - USA Patent and Trademark （商标）Office patent db Espcenet - Patent information database from the European Paten

36、t Office (worldwide coverage) The Delphion Intellectual Property Network (IPN) for searching, viewing, and analyzing patent documents.,9、资源目录服务器或网页,BioCatalog - The BioCatalog at EBI Yellow BAGI - Bio Access Guide to the Internet at Houston University Software library from G DBCAT - Databases catalo

37、g at INFOBIOGEN MBDL - Molecular Biology Database List Amos WWW links pageNucleic Acids Research database issue,Human （与人类基因有关的数据库）,CEPH-genotype databaseCEPH home page - a research laboratory which constructs maps of the human genomeGeneMap99 - A Gene Map of the Human Genome (NCBI) OMIM - Online Me

38、ndelian Inheritance in Man GENATLAS - Human genes atlas GeneClinics - Medical genetics knowledge base GDB - Human genes and genomic maps GeneCards - Db integrating information on human genes,Human,UDB - Unified db for Human genome mapping Ensembl - Human genome annotations site UCSC human genome wor

39、king draft TIGR HGI - TIGR Human Gene Index Human BAC Ends Database - Non-redundant human BAC end sequences Hs UniGene - Human transcripts in GenBank (EST clusters) STACK - Sequence Tag Alignment and Consensus Knowledgebase (Db of consensus human ESTs),Human,Allgenes.org - Human predicted gene index

40、/catalog GenLink - Human genetics resource GENOTK - Human cDNA db HUGE - Human Unidentified Gene-Encoded large proteins cDNA (KIAA.) CGAP - Cancer Genome Anatomy Project SCDb - Stem cell db,Human,HuGeMap - Human genome genetic and physical map data G3-RH - Stanford G3 and TNG radiation hybrid maps G

41、B4-RH - Genebridge4 (GB4) human radiation hybrid maps Radiation Hybrid Database - Radiation hybrid map data,Human chromosome 18,Chr1 - Human chromosome 1 at Rockefeller University Mirror at EBI Chr3 - Human chromosome 3 db at the University of Texas Health Science Center Chr7 - Human chromosome 7 db

42、 at Ontarios Hospital for Sick Children Chr8 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 8,Human chromosome911,Chr9 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 9 Chr9 - Human chromosome 9 db Chr10 SWISS-PROT list - Links to SWISS-PROT entries from huma

43、n chromosome 10 GTC Chr10 data - Human chromosome 10 data from Genome Therapeutics Corporation Chr11 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 11 11DB - Human chromosome 11 db at Imperial College (U.K.),Human chromosome1216,Chr12 SWISS-PROT list - Links to SWISS-PROT entrie

44、s from human chromosome 12 Chr13 - Human chromosome 13 db at Columbia Chr14 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 14 Chr15 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 15 Chr15 UBC - Human chromosome 15 WWW page at UBC Chr16 SWISS-PROT list - Link

45、s to SWISS-PROT entries from human chromosome 16,Human chromosome1619,Chr16 LANL - Human chromosome 16 db at Los Alamos National Laboratory Chr16 TIGR - Human chromosome 16 db at TIGR Chr17 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 17 Chr18 SWISS-PROT list - Links to SWISS-

46、PROT entries from human chromosome 18 Chr18 - Human chromosome 18 at Boston Childrens Hospital Chr19 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 19,Human chromosome2022,Chr20 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 20 Chr21 SWISS-PROT list - Links

47、to SWISS-PROT entries from human chromosome 21 Chr21 at RIKEN - Human chromosome 21 genome site at RIKEN (Japan) Chr21 at ERI - Human chromosome 21 genomic sequence db from the Eleanor Roosevelt Institute Chr22 SWISS-PROT list - Links to SWISS-PROT entries from human chromosome 22 Chr22 at Sanger -

48、Sanger Center chromosome 22 project Chr22 at HGC - Human genome center for chromosome 22,Human chromosomeXY（人类XY染色体）,ChrX SWISS-PROT list - Links to SWISS-PROT entries from human chromosome X IXDB - Integrated X chromosome db ChrY SWISS-PROT list - Links to SWISS-PROT entries from human chromosome Y

49、,Vertebrates （脊椎动物）,OMIA - Online Mendelian Inheritance in Animals MGI - Mouse Genome Informatics (includes *Mouse Genome Database (MGD)Mirrors in Australia | UK | Japan TIGR MGI - TIGR Mouse* Gene Index Mm UniGene - Mouse transcripts in GenBank (EST clusters) RatMAP - Rat genome db TIGR RGI - TIGR

50、Rat Gene Index Rn Unigene - Rat transcripts in GenBank (EST clusters) (以上与老鼠有关的基因数据库）,Vertebrates,BovBASE - Bovine genome db (in UK) BOVMAP - Bovine genome db (in France) （牛） Ark-Cat cat genome db (猫）HorseBASE - Horse genome db （马）DGP - Dog Genome Project （狗）PiGBASE - Pig genome db （猪）SheepBASE - Sh