生物信息学相关数据库资源介绍ppt课件

刘 吉 平Reference：biosino.org核酸及其相关数据库序列数据库、基因组相关数据库、核酸三维构造数据库、其他蛋白质相关数据库序列数据库、蛋白质三维构造数据库、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效力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、核酸三维构造数据库、其他蛋白质相关数据库序列数据库、蛋白质三维构造数据库、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效力器或网页1、核酸序列数据库、核酸序列数据库 BIOSINO 我国的核酸序列公共数据库我国的核酸序列公共数据库EMBL-EMBL Nucleotide sequence database EBI GenBank-GenBank Nucleotide Sequence database NCBIDDBJ-DNA Data Bank of Japan dbEST-Database of Expressed Sequence Tags 表达序列标签表达序列标签NCBI dbSTS-Database of Sequence Tagged Sites 序列序列标签位点标签位点 NCBI lGenomeWebHGMP-A catalogue of useful Web sites for Genomics with a set of collections of genome databases lGSDB-Genome Sequence database NCGRlGOLD-Genomes On-line dbl一些数据库的直接链接lNDB-Nucleic 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.lEPD-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 免疫遗传免疫遗传学学lISIS-Intron Sequence and Information System lRDP-Ribosomal db Project lgRNAs db-Guide RNA db lPLACE-Plant cis-acting regulatory DNA elements db lPlantCARE-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 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 类病毒lCre Transgenic Database-Cre transgenic mouse lines lTransgenic/Targeted Mutation Database-Information on transgenic animals and targeted mutations 蛋白质序列数据库蛋白质序列数据库PIR-international-The Protein Information Resource protein sequence 国际蛋白质信国际蛋白质信息中心，息中心，NBRF+JIPID+MIPs,PIR1PIR2PIR3PIR4 SWISS-PROT-SWISS-PROT annotated注释注释 protein sequence db SIB+EBI,EBI创建蛋白创建蛋白质专家分析系统质专家分析系统ExPASy，北京，北京MIPS Munich information 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 at 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 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 generated 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 Laboratory 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 curation 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-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 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 抗体lAustralian venom and toxin db 澳大利亚蛇毒lBacillus thuringiensis toxin specificity dbBtlTFII-Basal transcription factors 转录子lBlood group antigens in SWISS-PROT 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 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 lMonosacharide 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 expression 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-Ascidian 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,Localization 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 Finland 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 tetrahydrobiopterin deficiencies 缺乏四氢生物蝶呤lBLMbase-Human BLM mutation db Bloom snydromlBTKbase-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 db CFTR 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lFBN1 mutation-Human fibrillin 1 mutation db Marfan syndrome lG6PD-Human G6PD deficiency resource lGalt mutation-Human galactose-1-phosphate uridylyltransferase mutation db GalactosemialHEXAdb-Human Hexosaminidase A mutation db Tay-sachs disease lIL2RGbase-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 lNeuromuscular 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 mutations 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 Information 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-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-referencing of model organism genetics with mammalian phenotypes lTreeBASE-Relational db of phylogenetic informationlThe Tree of life-Collection of WWW pages on phylogeny and biodiversity of organisms 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 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 lSoftware library from Genamics lDBCAT-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-Online 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 genome 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 lAllgenes.org-Human predicted gene index/catalog 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-RH-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 Hospital 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-Human 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 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 16lChr16 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 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 21 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 chromosome 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 Database MGDMirrors 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 l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 db 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lFishBase-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-Pilot-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 sequences lDrosophila SWISS-PROT list-Links to Drosophila SWISS-PROT entries 果蝇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 binding sites lMosquito Genomics 蚊子lWormBase-C.elegans db Mirror at Sanger lC.elegans WWW server-at University of Texas Southwestern 线虫lACeDb-Caenorhabditis elegans db lC.elegans Mitochondrial Directory-Data on C.elegans genes for mitochondrial proteins lC.elegans EST-C.elegans EST db 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 lDicty_cDB-Dictyostelium discoideum cDNA project lCone shells Web site lParasite genomes db and resources 寄生虫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 falciparum Genome db lP.falciparum-Plasmodium falciparum Gene Sequence Tag project 疟原虫lMAD-Malaria Antigen db lMalaria parasite metabolic pathways lLGN-Leishmania Genome Network 利什曼虫lTrypanosoma brucei genome project 锥体虫lTrypanosoma cruzi genome project lkDNA-Kinetoplast Minicircle Sequence db lNAL-AGIS-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 lMATDB-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 农作物lCottonDB-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 lRice-research.org-Monsanto rice genome site lTIGR OsGI-TIGR Rice Gene Index lTIGR GmGI-TIGR Soybean Gene Index 大豆lSnapdragon A.majus web site lSorghumDB-Sorghum genome db 高粱lSoyBase-Soybean genome db lSoyBase metabolic db-Metabolic subset of the soybean genome db lTIGR LeGI-TIGR Tomato Gene Index 西红柿lDendrome-Forest trees genome db 树林植物lFGSC-Fungal Genetics Stock Center lFGR-Fungal Genome Resource lYeast SWISS-PROT list-Links to S.cerevisiae WWW sites and to SWISS-PROT entries lSGD-Saccharomyces genome db 酵母lYPD-Yeast protein db lMitBASE-Pilot-Db of S.cerevisiae nuclear genes involved in mitochondrial biogenesis 酵母lYeast snoRNA-Yeast small nucleolar RNAs db lYTPdb-Yeast Transport Protein db 酵母lPathCalling-Yeast protein-protein interaction db lAspergillus web site lC.albicans SWISS-PROT list-Links to C.albicans WWW sites and to SWISS-PROT entries lCandida albicans-Candida albicans server at the Univ.of Minnesota 假丝酵母lNGP-Neurospora crassa genome project脉孢菌lPC-Pneumocystis carinii genome project lS.pombe SWISS-PROT list-Links to S.pombe WWW sites and to SWISS-PROT entries lS.pombe NIH-Fission yeast S.pombe server at the NIHlPhycomyces Web site-Resource site for scientists working on Phycomyces llEMGlib-Completely sequenced bacterial genomes and the yeast genome lICB-Identification and Classification of Bacteria lWDCM-World Data Center for Microorganisms lList of Bacterial Names with Standing in Nomenclature lMDB-TIGR Microbial db l-Genome information broker for Microbial genomes lHOBACGEN-Homologous Bacterial Genes db lComparison of the transport capabilities of bacterial genomes-from Ian Paulsen lBPGD-Bacterial polysaccharide gene db lBacterial quorum sensing lMicrobeWorld-Educational site on microbes lE.coli SWISS-PROT list-Links to E.coli WWW sites and to SWISS-PROT entries lEcoWeb/EcoGene-Very comprehensive E.coli db lECCE-E.coli Cell Envelope Protein Data Collection lECDC-E.coli db collection lEcoCyc-Encyclopedia of E.coli genes and metabolismlGenProtEC-E.coli genome and proteome db lColibri-E.coli genome db from Pasteur Insitute lECGC-E.coli Genome Center at Wisconsin University 大肠杆菌lDDBJ E.coli-E.coli home page at DDBJ lB.subtilis SWISS-PROT list-Links to B.subtilis WWW sites and to SWISS-PROT entries lSubtiList-Bacillus subtilis genomic db lNRSub-Bacillus subtilis non-redundant db Mirror in JapanlMicado-Microbial advanced db B.subtilis+E.coli previously known as MadBase lBSORF-Japanese server on B.subtilis lA.actinomycetemcomitans-Actinobacillus actinomycetemcomitans strain HK1651 genome project lB.stearothermophilus-Bacillus stearothermophilus strain 10 genome project lB.pertussis-Bordetella pertussis genome WWW site lBbDB-TIGR Borrelia burgdorferi genome db liBGD-Integrated Buchnera genome db lB.cepacia-Burkholderia cepacia genome project lChlamydia-Chlamydia pneumoniae and trachomatis lC.muridarum-TIGR Chla