Fong Christine, Rohmer Laurence, Radey Matthew, Wasnick Michael, Brittnacher Mitchell J
Department of Genome Sciences, University of Washington, Box 357710, Seattle, Washington 98195, USA.
BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.
The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes.
PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function.
PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at http://www.nwrce.org/psat.
原核生物基因组间基因顺序的保守性能够为基因功能、蛋白质相互作用或基因组进化事件提供有价值的见解。虽然有一些工具可用于可视化和比较研究中的基因组间的基因顺序，但很少有工具支持对大量基因组进行高效且有条理的分析。原核生物序列同源性分析工具（PSAT）是一个用于比较多个原核生物基因组间基因邻域的网络工具。
PSAT利用一个预先加载了基因注释、BLAST比对结果和基因聚类分数的数据库，旨在帮助识别保守基因顺序区域。研究人员使用PSAT网络界面在参考基因组中找到感兴趣的基因，并有效地检索在其他细菌基因组中发现的序列同源物。该工具生成所选基因周围的基因组邻域图以及每个比较基因组中其同源物的相应区域图。每个区域中的同源物用颜色编码，以帮助用户分析不同基因组间的基因顺序。与基于比对分数阈值过滤序列同源数据的常见比较分析方法不同，PSAT利用同源物的基因上下文信息，包括那些比对分数较弱的同源物，从而实现更灵敏的分析。用于约束或排序结果的功能旨在帮助研究人员以有条理的方式浏览来自大量比较基因组的结果。PSAT已被证明有助于识别基因直系同源物和潜在的功能基因簇，以及检测可能导致功能丧失的基因组修饰。
PSAT使研究人员能够研究多个基因组局部基因组邻域内的基因顺序。可通过任何网络浏览器使用供公众使用的PSAT网络服务器，无需设置或安装客户端软件，即可对越来越多的参考基因组进行分析。有兴趣为分析公共服务器无法获取的基因组而设置PSAT本地版本的研究人员可免费获取源代码。可在http://www.nwrce.org/psat上找到公共网络服务器的访问权限和获取源代码的说明。
