mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.
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DOI：
10.1093/nar/gkq326
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发表时间：
2010-07
影响因子：
14.9
通讯作者：
Deng Z
中科院分区：
文献类型：
--
作者：
Shao Y;He X;Harrison EM;Tai C;Ou HY;Rajakumar K;Deng Z
mGenomeSubtractor对参考细菌基因组与多个用户选择的基因组进行基于mpiBLAST的比较，以研究菌株可变辅助区。通过并行计算架构，mGenomeSubtractor能够在一分钟内在DNA或氨基酸水平上对多个受试者基因组进行分段参考基因组的快速BLAST搜索。除了比较蛋白质编码序列外，所提供的高度灵活的基于滑动窗口的基因组片段化方法可用于鉴定基因内或基因间的短的独特序列。mGenomeSubtractor为探索已识别的核心和附属区域提供了强大的示意图输出，包括针对移动的遗传元件、毒力因子或细菌必需基因的数据库的搜索，G+C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还允许基于可用基因组的物种特异性基因库的现成定义。泛基因组阵列可以很容易地开发使用高效的寡核苷酸设计工具。这种简单的高通量计算机“消减杂交”分析工具将支持数量迅速增加的比较细菌基因组学研究，旨在定义不同细菌物种的进化谱系、表型、致病型、环境适应和/或疾病相关性的基因组生物标志物。mGenomeSubtractor免费提供给所有用户，无需任何登录要求：http://bioinfo-mml.sjtu.edu.cn/mGS/。
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/.
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影响因子：
5.8
作者：
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通讯作者：
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