第1章生物信息学网络资源研究报告.ppt

第三章 生物信息学网络资源(1) NCBI简介 Entrez系统 NCBI综合数据库 美国国家生物技术信息中心(National Center for Biotechnology Information，简称NCBI）创建于1988年 。 1991年，NCBI开发了Entrez数据库查询系统，用于对GenBank等分子生物学和生物医学文献摘要(Medline)等数据库的查询 (Schuler et al, 1996)。 Entrez系统的使用方法 练习 利用Enterz查找human CCL18基因的核酸\蛋白质RefSeq序列，保存为FASTA格式，记录RefSeq的Accession numbers。 练习 在PubMed中搜索human CCL18基因研究的报道（2000年以后）,列出检索到的篇目，并试图找到一至两篇全文。 第一次作业 利用Enterz查找human CCL18，human cxcl1基因的核酸\蛋白质RefSeq序列，保存为FASTA格式，记录从GeneBank获得的序列信息。 在PubMed中搜索human CCL18基因研究的报道（2000年以后）,列出检索到的篇目，并试图找到一至两篇全文。 OMIM is… Online Mendelian Inheritance in Man catalog of human genes and genetic disorders edited by Dr. Victor McKusick, others at JHU Books is… searchable resource of on-line books TaxBrowser is… browser for the major divisions of living organisms (archaea, bacteria, eukaryota, viruses) taxonomy information such as genetic codes molecular data on extinct organisms Structure site includes… Molecular Modelling Database (MMDB) biopolymer structures obtained from the Protein Data Bank (PDB) Cn3D (a 3D-structure viewer) vector alignment search tool (VAST) FASTA format Entrez Gene (top of page) Note that links to many other RBP4 database entries are available Entrez Gene (middle of page) Entrez Gene (bottom of page) Example of how to access sequence data: HIV-1 pol There are many possible approaches. Begin at the main page of NCBI, and type an Entrez query: hiv-1 pol Searching for HIV-1 pol: Following the “genome” link yields a manageable four results Example of how to access sequence data: HIV-1 pol For the Entrez query: hiv-1 pol there are about 40,000 nucleotide or protein records (and 100,000 records for a search for “hiv-1”), but these can easily be reduced in two easy steps: --specify the organism, e.g. hiv-1[organism] --limit the output to RefSeq! only 1 RefSeq over 100,000 nucleotide entries for HIV-1 Four ways to access DNA and protein sequences [1] Entrez Gene with RefSeq [2] UniGene [3] European Bioinformatics Institute