Treangen Todd J, Messeguer Xavier
Dept. of Computer Science, Technical University of Catalonia, Barcelona, Spain.
BMC Bioinformatics. 2006 Oct 5;7:433. doi: 10.1186/1471-2105-7-433.
Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons.
To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes) in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations.
M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.
由于全基因组鸟枪法测序和组装技术的最新进展，解码生物体DNA的财务成本已大幅降低，导致近期基因组测序项目激增。相关基因组数据的增加将允许通过多个全基因组比较对密切相关物种的进化进行深入研究。
为便于此类比较，我们展示了一种交互式多基因组比较和比对工具M-GCAT，它可以在密切相关的物种中高效构建多基因组比较框架。M-GCAT能够在标准计算机上几分钟内比较并识别多达20个密切相关细菌物种中的高度保守区域，一小时内可处理多达90个（包含来自15个已发表肠杆菌基因组的75个克隆基因组）。M-GCAT还集成了一个新颖的比较基因组学数据可视化界面，允许用户全局和局部检查和审视保守区域及基因注释。
M-GCAT是一种交互式比较基因组学工具，非常适合快速生成密切相关物种之间的多基因组比较框架和比对。M-GCAT可免费下载供学术和非商业使用，网址为：http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html。
