生物信息学 相关数据库资源介绍,刘 吉 平 Reference： www.biosino.org,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 - GenBank 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 genome databases GSDB - 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 frequency 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-acting 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 - 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/Targeted 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 information,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 ProDom - 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 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 - 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 structure 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 structural 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 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 db CANSITE - Signal Transductions Web SPAD - 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 aminoacyl-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 thuringiensis toxin specificity db TFII - 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