Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, P. R. China.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W194-200. doi: 10.1093/nar/gkq326. Epub 2010 Apr 30.
mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico 'subtractive hybridization' analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/.
mGenomeSubtractor 基于 mpiBLAST 对参考细菌基因组与多个用户选择的基因组进行比较，以研究菌株可变附件区域。mGenomeSubtractor 具有并行计算架构，能够在一分钟内针对 DNA 或氨基酸水平的多个主题基因组对分段参考基因组进行快速 BLAST 搜索。除了比较蛋白质编码序列外，还可以使用高度灵活的基于滑动窗口的基因组碎片化方法来识别基因内或基因之间的短独特序列。mGenomeSubtractor 提供了强大的原理图输出，用于探索已识别的核心和附件区域，包括针对移动遗传元件、毒力因子或细菌必需基因数据库的搜索、GC 含量和二核苷酸分布偏倚的检查，以及集成的引物设计工具。mGenomeSubtractor 还允许根据可用基因组轻松定义特定于物种的基因库。可以使用高效的寡核苷酸设计工具轻松开发泛基因组数组。这个简单的高通量计算机“减法杂交”分析工具将支持越来越多的比较细菌基因组学研究，旨在定义进化谱系、表型、病原型、环境适应和/或不同细菌物种疾病关联的基因组生物标志物。mGenomeSubtractor 免费提供给所有用户，无需登录，网址为：http://bioinfo-mml.sjtu.edu.cn/mGS/。
