很好生物信息相关数据库资源介绍课件.ppt

1、1.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）2.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）3.基因或蛋白质一些特定数据库4.糖类及其相关数据库5.蛋白质翻译后修饰相关数据库6.基因表达数据库7.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9.资源目录服务器或网页1.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）2.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

2、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）3.基因或蛋白质一些特定数据库4.糖类及其相关数据库5.蛋白质翻译后修饰相关数据库6.基因表达数据库7.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9.资源目录服务器或网页1）、核酸序列数据库）、核酸序列数据库l BIOSINO 我国的核酸序列公共数据库lEMBL-EMBL Nucleotide sequence database(EBI)lGenBank-GenBank Nucleotide Sequence database(NCBI)lDDBJ-DNA Data Bank of Jap

3、an ldbEST-Database of Expressed Sequence Tags （表达序列标签）(NCBI)ldbSTS-Database of Sequence Tagged Sites（序列标签位点）(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一些数据库的直接链接lNDB-Nu

4、cleic Acid Databank(3D structures)lBNASDB-Nucleic acid structure db from University of Pune lAsDb-Aberrant Splicing db（异常拼接）（异常拼接）lACUTS-Ancient conserved untranslated DNA sequences db lCodon Usage Db -The frequency of codon use in each organism is made searchable through this World Wide Web site.lE

5、PD-Eukaryotic Promoter db（真核启动子）（真核启动子）lHOVERGEN-Homologous Vertebrate Genes db（同源（同源脊椎动物）脊椎动物）lIMGT-ImMunoGeneTics db Mirror at EBI（免疫遗传学免疫遗传学）lISIS-Intron Sequence and Information System lRDP-Ribosomal db Project lgRNAs db-Guide RNA db lPLACE-Plant cis-acting regulatory DNA elements db lPlantCARE-

6、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（编辑）（编辑）from the University of Bayreuth luRNADB-uRNA db lRNA editing-RNA editi

7、ng 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)（类病毒）lCre Transgenic Database-Cre transgenic mouse lines lTransgenic/Targeted Mutation Database-Information

8、on transgenic animals and targeted mutations 蛋白质序列数据库蛋白质序列数据库lPIR-international-The Protein Information Resource(protein sequence)（国际蛋白质信息中心，（国际蛋白质信息中心，NBRF+JIPID+MIPs,PIR1PIR2PIR3PIR4)）lSWISS-PROT-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)lMIPS (Munich information

9、center for protein sequence)（德国慕尼黑蛋白质序列信息中心德国慕尼黑蛋白质序列信息中心）lPROSITE-PROSITE dictionary of protein sites and patterns lInterPro-Integrated Resources of Proteins Domains and Functional Sites lBLOCKS-BLOCKS db lDOMO-Protein domain db(Automatically generated)lPfam-Protein families db(HMM derived)Mirror a

10、t Sanger lPRINTS-Protein Motif fingerprint db lProDom-Protein domain db(Automatically generated)lPROTOMAP-An automatic hierarchical（分等级）（分等级）classification of SWISS-PROT proteins lSBASE-SBASE domain db(Protein domain sequence library)lSMART-Protein signalling and extracellular domain patterns(Simple

11、 Modular Architecture Research Tool)lProClass-Protein sequence alignments and curation of protein families lPDB-Protein Data Bank Mirrors in EBI lBioMagResBank Repository（知识）（知识）for data on proteins,peptides,and nucleic acids from NMR spectroscopy（光谱学）（光谱学）lSWISS-MODEL Repository-Automatically gener

12、ated protein models db lModBase-Db of comparative protein structure models lCATH-UCL BSM structural classification of proteins lSCOP-Structural classification of proteins Mirror at USA|Israel|Singapore|Australia lMol_R_Us-Molecules R Us,browser for PDB lBMM Domain Server-Biomolecular Modelling Labor

13、atory(ICRF)protein domain server lPRESAGE-Collaborative resource for structural genomics lSBASE-SBASE domain db(Protein domain sequence library)lSMART-Protein signalling and extracellular（细胞外）（细胞外）domain patterns(Simple Modular Architecture Research Tool)lProClass-Protein sequence alignments and cur

14、ation of protein families lKabat-Kabat db of protein of immunological interest lPMD-Protein Mutant db lWORLD-2DPAGE-A complete index of 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-

15、Protein interaction dblCANSITE-Signal Transductions（信号传导）（信号传导）WeblSPAD-Signaling pathway db lCSNDB-Cell Signaling Networks db lDPInteract-DNA-Proteins interactions dblAAA-AAA family of ATPases server Acetylcholinesterases lALDH-Aldehyde dehydrogenase（醛脱氢酶，l 醛氧化酶）gene superfamily db lAminoacyl-tRNA

16、synthetases in SWISS-PROT-List of aminoacyl-tRNA synthetases in SWISS-PROT lAARSDB-Aminoacyl-tRNA synthetases db lAllergens in SWISS-PROT-Nomenclature and index（命名和索引）of allergens（过敏原）in SWISS-PROT lAMSDb-Antimicrobial sequences db（抗菌）lAntibody resource page-Links to antibody related Web resources（抗

17、体）lAustralian venom and toxin db（澳大利亚蛇毒）lBacillus thuringiensis toxin specificity db（Bt）lTFII-Basal transcription factors（转录子）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

18、 lCAZy-Carbohydrate-Active enZYmes Web site lCBS domain Cystathionine（胱硫醚,丙氨酸丁氨酸硫醚）Beta 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

19、GroES chaperonins lConotoxins-Information on conotoxins from a Web site on cone 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 lMono

20、sacharide browser-Space filling Fischer projection for monosaccharides（单糖）lO-GlycBase-O-glycosylated（使(蛋白质)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 expr

21、ession in Xenopus lBodyMap-Human and mouse gene expression data lEpoDB-Genes expressed in vertebrate RBC lFlyView-Drosophila development and genetics（果蝇）lGene Expression Database(GXD)-Mouse gene expression and genomics（鼠）lKidney Development Database Kidney（肾）development and gene expressionlMAGEST-As

22、cidian(Halocynthia roretzi)gene expression patterns lMouse Atlas and Gene Expression Database-Spatially-mapped gene expression data lPEDB-Normal and aberrant prostate（正常、异常前列腺）gene expression lTooth Development Database-Gene expression in dental tissue lTRIPLES-TRansposon-Insertion Phenotypes,Locali

23、zation and Expression in 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（单核苷酸多态性数据库）lList of mutation databases from OMIMl List of mutation databases from IMT(F

24、inland)lADB-Albinism db(Mutations in human genes causing albinism（白化病）)lAlpha-glucosidase-Information about human acid alpha-glucosidase(GSD-II)lAR mutations-Human androgen receptor mutation db lAntithrombin mutation db（抗凝血突变）lAsthma and Allergy gene db（哮喘和过敏）lBIOMDB-Db of mutations causing tetrahyd

25、robiopterin deficiencies（缺乏四氢生物蝶呤缺乏四氢生物蝶呤lBLMbase-Human BLM mutation db(Bloom snydrom)lBTKbase-Human BTK mutation db(X-linked agammaglobulinemia)（血中丙球蛋白贫乏）lCD40Lbase-Human CD40 ligand mutation db lCOL1/3 mutation-Human Type I and III collagen mutation db lCFTR mutation-Human cystic fibrosis mutation

26、 db(CFTR)（囊肿性纤维化，属遗传性胰腺病囊肿性纤维化，属遗传性胰腺病）lEMD db-Human Emerin(EMD)mutation db(Emery-Dreifuss muscular dystrophy)肌肉萎缩症肌肉萎缩症lKMeyeDB-Eye disease genes db lFVII mutation-Human Factor VII mutation db lHAMSTeRS-Human Factor VIII mutation db(Haemophilia A)lHAeMB-Human Factor IX mutation db(Haemophilia B)血友病

27、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)lIL2RGbase-Human IL2RG(Interleukin-2 receptor gamma)m

28、utation 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 lNeuromuscular diseases web site lNCL-Neuronal Ceroid Lipofuscinoses mutation db

29、 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 mutations lPAHdb-Human phenylalanine hydroxylase(PAH)mutation db lPAX6 mutation-Human

30、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 Information Network lRetina International Scientific Newsletter-Information on Retinal genes,prot

31、eins 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-Human von Willebrand factor(vWF)mutation db lWRN-Human WRN mutation db(Warner disease)lWT1 mutation-Human WT1 mutati

32、on db lX-ALD mutation-Human ABCD1 mutation db lClusters of Orthologous Groups(COG)-Phylogenetic classification of proteins from 21 complete genomes lXREFdb-Cross-referencing of model organism genetics with mammalian phenotypes lTreeBASE-Relational db of phylogenetic informationlThe Tree of life-Coll

33、ection of WWW pages on phylogeny and biodiversity of organisms http:/phylogeny.arizona.edu/tree/lDPD-DNA Patent db lAg Patents-Agricultural Biotechnology patents from the USDA（农业生物技术专利）lUSPTO patent db-USA Patent and Trademark（商标）Office patent db lEspcenet-Patent information database from the Europe

34、an 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 lSoftware library from G lDBCAT-Databases catalog at INFOBIOG

35、EN 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-Online Mendelian Inheritance in Man lGENATLAS

36、-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 genome working draft lTIGR HGI-TIGR Human Gene Index lHum

37、an 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)lAllgenes.org-Human predicted gene index/catalog lGenLink-Human genetics resource lGENOTK-Human cDNA d

38、b 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-RH-Genebridge4(GB4)human radiation hybrid maps lRadiation Hybrid Database

39、-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 Hospital for Sick Children lChr8 SWISS-PROT list-Links to SWISS-PROT entries from human chr

40、omosome 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-Human chromosome 10 data from Genome Therapeutics Corporation lChr11 SWISS-PROT list-Links to SW

41、ISS-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 13 db at Columbia lChr14 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 14 lChr15 SWI

42、SS-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 16lChr16 LANL-Human chromosome 16 db at Los Alamos National Laboratory lChr16 TIGR-Human chromosome 16 db at TIGR

43、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 at Boston Childrens Hospital lChr19 SWISS-PROT list-Links to SWISS-PROT entries from human chromosome 19 lChr20 SWISS-PRO

44、T 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 21 genome site at RIKEN(Japan)lChr21 at ERI-Human chromosome 21 genomic sequence db from the Eleanor Roosevelt Institute lChr22 SWI

45、SS-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 chromosome 22 lChrX SWISS-PROT list-Links to SWISS-PROT entries from human chromosome X lIXDB-Integrated X chromosome db lChrY SWISS-PROT list-

46、Links to SWISS-PROT entries from human chromosome YlOMIA-Online Mendelian Inheritance in Animals lMGI-Mouse Genome Informatics(includes*Mouse Genome 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

47、lTIGR RGI-TIGR Rat Gene Index lRn Unigene-Rat transcripts in GenBank(EST clusters)(以上与老鼠有关的基因数据库）lBovBASE-Bovine genome db(in UK)lBOVMAP-Bovine genome db(in France)（牛）lArk-Cat cat genome db(猫）lHorseBASE-Horse genome db （马）lDGP-Dog Genome Project （狗）lPiGBASE-Pig genome db （猪）lSheepBASE-Sheep genome d

48、b(also known as SheepMap)Mirror in UK （羊）lMIS-Mendelian Inheritance in Sheep lChickGBASE-Chicken genome db（鸡）lFugu-HGMP Resource Centre Fugu Project(Fugu rubripes)（河豚）lMedakafish-Mekada fish(Oryzias latipes)server lArk-Tilapia-Tilapia（罗非鱼）mossambica genome db lThe fish net-Zebrafish server（斑马鱼）lFish

49、Base-Global information system on fishes lGOBASE-Organelle Genome Database lMitoDat-Mendelian Inheritance and the Mitochondrion db(mitochondrial nuclear genes)lMITOMAP-Human mitochondrial genome db lMmtDB-Metazoa mitochondrial DNA variants db（后生动物）lMitBASE-Integrated mitochondrial DNA db lMitBASE-Pi

50、lot-Db of S.cerevisiae nuclear genes involved in mitochondrial biogenesis 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 sequenc