生物信息学相关数据库资源介绍.ppt

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1、生物信息学相关数据库资源介绍,生物信息学相关数据库资源,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）蛋白质相关数据库（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-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,一、核酸及其相关数据库,1、核酸序列数据库 EMBL-EMBL Nucleotide sequence database(EBI)*GenBank-GenBan

2、k Nucleotide Sequence database(NCBI)*DDBJ-DNA Data Bank of Japan*BIOSINO 我国的核酸序列公共数据库dbEST-Database of Expressed Sequence Tags(NCBI)dbSTS-Database of Sequence Tagged Sites(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 ge

3、nome databasesGSDB-Genome Sequence database(NCGR)GOLD-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 ACUTS-Ancient conserved untranslated DNA sequences db Codon Usage Db-The freq

4、uency of codon use in each organism is made searchable through this World Wide Web site.EPD-Eukaryotic Promoter db HOVERGEN-Homologous Vertebrate Genes db IMGT-ImMunoGeneTics db Mirror at EBI ISIS-Intron Sequence and Information System RDP-Ribosomal db Project gRNAs db-Guide RNA db PLACE-Plant cis-a

5、cting regulatory DNA elements db,其它,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 from the University of Bayreuth uRNADB

6、-uRNA db,其他,RNA editing-RNA editing site RNAmod db-RNA modification db TelDB-Multimedia Telomere Resource TRADAT-TRAnscription Databases and Analysis Tools Subviral RNA db-Small circular RNAs db(viroid and viroid-like),Transgenics,Cre Transgenic Database-Cre transgenic mouse lines Transgenic/Targete

7、d Mutation Database-Information on transgenic animals and targeted mutations,二.蛋白质序列和相关数据库,SWISS-PROT-SWISS-PROT annotated protein sequence db PIR-international-The Protein Information Resource(protein sequence)MIPS-Martinsried institute for protein sequence and homology data and yeast genome inform

8、ation,蛋白质及其相关数据库,PROSITE-PROSITE dictionary of protein sites and patterns InterPro-Integrated Resources of Proteins Domains and Functional Sites BLOCKS-BLOCKS db DOMO-Protein domain db(Automatically generated)Pfam-Protein families db(HMM derived)Mirror at Sanger PRINTS-Protein Motif fingerprint db P

9、roDom-Protein domain db(Automatically generated)PROTOMAP-An automatic hierarchical classification of SWISS-PROT proteins SBASE-SBASE domain db(Protein domain sequence library)SMART-Protein signalling and extracellular domain patterns(Simple Modular Architecture Research Tool)ProClass-Protein sequenc

10、e 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-Repository for data on proteins,peptides,and nucleic acids from NMR spectroscopy SWISS-MODEL Repository-Automatically generated protein models db ModBase-Db of comparative protein structur

11、e models CATH-UCL BSM structural classification of proteins SCOP-Structural classification of proteins 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 st

12、ructural genomics,蛋白质三维结构和相关数据库,SBASE-SBASE 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 Kabat-Kabat db of protein of immunological

13、interest PMD-Protein Mutant db,蛋白质二维凝胶电泳数据库,WORLD-2DPAGE-A complete index of 2D-PAGE db and servers Phoretix links-Phoretix page of links to 2D gel db,三、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 Tr

14、ansductions WebSPAD-Signaling pathway db CSNDB-Cell Signaling Networks db,四、DNA和蛋白质相互作用数据库,DPInteract-DNA-Proteins interactions db,五、特定基因或蛋白质的数据库,AAA-AAA family of ATPases server Acetylcholinesterases ALDH-Aldehyde dehydrogenase gene superfamily db Aminoacyl-tRNA synthetases in SWISS-PROT-List of am

15、inoacyl-tRNA synthetases in SWISS-PROT AARSDB-Aminoacyl-tRNA synthetases db Allergens in SWISS-PROT-Nomenclature and index of allergens in SWISS-PROT,特定基因或蛋白质的数据库,AMSDb-Antimicrobial sequences db Antibody resource page-Links to antibody related Web resources Australian venom and toxin db Bacillus th

16、uringiensis toxin specificity dbTFII-Basal transcription factors Blood group antigens in SWISS-PROT BCGD-Breast cancer genes db from MBCR 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 enZYmes Web site CBS domain-Cystathioni

17、ne Beta Synthase domain WWW page CD antigens in SWISS-PROT-Nomenclature for surface proteins of human leucocytes(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 chaperonins Conotoxins-Information on conotoxins from a Web site o

18、n cone shells。etc。,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 Monosacharide browser-Space filling Fischer projection for monosaccharides,蛋

19、白质翻译后修饰相关数据库,O-GlycBase-O-glycosylated proteins db PhosphoBase-Phosphorylation sites db RESID-Db of Amino Acid Modifications,基因表达数据库,ASDB-Protein products and expression patterns of alternatively-spliced genes Axeldb-Gene expression in Xenopus BodyMap-Human and mouse gene expression data EpoDB-Genes

20、 expressed in vertebrate RBC FlyView-Drosophila development and genetics Gene Expression Database(GXD)-Mouse gene expression and genomics Kidney Development Database-Kidney development and gene expression,基因表达数据库,MAGEST-Ascidian(Halocynthia roretzi)gene expression patterns Mouse Atlas and Gene Expre

21、ssion Database-Spatially-mapped gene expression data PEDB-Normal and aberrant prostate gene expression Tooth Development Database-Gene expression in dental tissue TRIPLES-TRansposon-Insertion Phenotypes,Localization and Expression in Saccharomyces,人类基因突变及疾病相关数据库,HMGD-Human Gene Mutation db SVD-Seque

22、nce variation db HGBASE-Human Genic Bi-Allelic Sequences db The SNP consortium dbSNP-Human single nucleotide polymorphism(SNP)db 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)Alpha-glucosidas

23、e-Information about human acid alpha-glucosidase(GSD-II)AR mutations-Human androgen receptor mutation db Antithrombin mutation db Asthma and Allergy gene db BIOMDB-Db of mutations causing tetrahydrobiopterin deficiencies BLMbase-Human BLM mutation db(Bloom snydrom),人类基因突变及疾病相关数据库,BTKbase-Human BTK m

24、utation db(X-linked agammaglobulinemia)CD40Lbase-Human CD40 ligand mutation db COL1/3 mutation-Human Type I and III collagen mutation db CFTR mutation-Human cystic fibrosis mutation db(CFTR)EMD db-Human Emerin(EMD)mutation db(Emery-Dreifuss muscular dystrophy)KMeyeDB-Eye disease genes db,人类基因突变及疾病相关

25、数据库,FVII mutation-Human Factor VII mutation db HAMSTeRS-Human Factor VIII mutation db(Haemophilia A)HAeMB-Human Factor IX mutation db(Haemophilia B)FBN1 mutation-Human fibrillin 1 mutation db(Marfan syndrome)G6PD-Human G6PD deficiency resource Galt mutation-Human galactose-1-phosphate uridylyltransf

26、erase 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)LQTSdb-Long QT sy

27、ndrome 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 mutation db-University of Tokyo p53

28、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 mutation db RAG2base-Human RAG2 mutation db RB1b

29、ase-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-Cardiff-Rotterdam Tuberous Sclerosis(TS)db(Tuberin;TSC2)TGDB-

30、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 mutation db,进化相关数据库及资源,Clusters of Orthologous Groups(COG)-Phylogenetic classification of

31、 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 phylogeny and biodiversity of organisms,专利数据库,DPD-DNA Patent db Ag Patents-Agricultural Biote

32、chnology patents from the USDA USPTO patent db-USA Patent and Trademark Office patent db Espcenet-Patent information database from the European Patent Office(worldwide coverage)The Delphion Intellectual Property Network(IPN)for searching,viewing,and analyzing patent documents.,资源目录服务器或网页,BioCatalog-

33、The BioCatalog at EBI Yellow BAGI-Bio Access Guide to the Internet at Houston University Software library from G DBCAT-Databases catalog at INFOBIOGEN MBDL-Molecular Biology Database List Amos WWW links pageNucleic Acids Research database issue,Human,CEPH-genotype databaseCEPH home page-a research l

34、aboratory which constructs maps of the human genomeGeneMap99-A Gene Map of the Human Genome(NCBI)OMIM-Online Mendelian 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,

35、UDB-Unified db for Human genome mapping Ensembl-Human genome annotations site UCSC human genome working 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 K

36、nowledgebase(Db of consensus human ESTs),Human,Allgenes.org-Human predicted gene index/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 a

37、nd physical map data G3-RH-Stanford G3 and TNG radiation hybrid maps GB4-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

38、 of Texas Health Science Center Chr7-Human chromosome 7 db 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 SWI

39、SS-PROT list-Links to SWISS-PROT entries from human 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 S

40、WISS-PROT list-Links to SWISS-PROT entries 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

41、 UBC Chr16 SWISS-PROT list-Links 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-PR

42、OT list-Links to SWISS-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-P

43、ROT list-Links 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 Sa

44、nger-Sanger Center chromosome 22 project Chr22 at HGC-Human genome center for chromosome 22,Human chromosomeXY,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 DRESH-Human

45、 cDNA clones homologous to Drosophila mutant genes,Vertebrates,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 gen

46、ome db TIGR RGI-TIGR Rat Gene Index Rn Unigene-Rat transcripts in GenBank(EST clusters),Vertebrates,BovBASE-Bovine genome db(in UK)BOVMAP-Bovine genome db(in France)Ark-Cat-Cat genome db HorseBASE-Horse genome db DGP-Dog Genome Project PiGBASE-Pig genome db SheepBASE-Sheep genome db(also known as Sh

47、eepMap)Mirror in UK MIS-Mendelian Inheritance in Sheep ChickGBASE-Chicken genome db,Vertebrates,Fugu-HGMP Resource Centre Fugu Project(Fugu rubripes)Medakafish-Mekada fish(Oryzias latipes)server Ark-Tilapia-Tilapia mossambica genome db The fish net-Zebrafish server FishBase-Global information system

48、 on fishes,Mitochondrion and chloroplast,GOBASE-Organelle Genome Database MitoDat-Mendelian Inheritance and the Mitochondrion db(mitochondrial nuclear genes)MITOMAP-Human mitochondrial genome db MmtDB-Metazoa mitochondrial DNA variants db MitBASE-Integrated mitochondrial DNA db MitBASE-Pilot-Db of S

49、.cerevisiae nuclear genes involved in mitochondrial biogenesis HvrBase-Primates mtDNA control region sequences compilation,Mitochondrion and chloroplast,MOUSE-Mitochondrial and Other Useful SEquences(human and apes mit.DNA db)MITOP-Mitochondrial proteins,genes and diseases AMmtDB-Metazoan mitochondr

50、ial DNA sequences,Insects,Drosophila SWISS-PROT list-Links to Drosophila SWISS-PROT entries FlyBase-Drosophila genetic and molecular db Mirror at EBI FlyView-Drosophila image db GIFTS-Gene Interactions in the Fly Trans-World Server FlyNets-Db of molecular interactions in Drosophila melanogaster SOS-