GMATo: A novel tool for the identification and analysis of microsatellites in large genomes.
GMATo: A novel tool for the identification and analysis of microsatellites in large genomes.
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DOI：
10.6026/97320630009541
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发表时间：
2013
期刊：
影响因子：
1.9
通讯作者：
Luo Z
中科院分区：
文献类型：
--
作者：
Wang X;Lu P;Luo Z
简单序列重复序列(SSR)，又称微卫星，在遗传标记开发和基因组应用中具有重要意义。越来越多的大基因组的全序列不断增加，为在计算机上挖掘SSR提供了来源。然而，现有的SSR挖掘工具不能有效地处理大基因组，并且不能产生或不能产生很差的统计数据。全基因组微卫星分析工具(GMATo)是一种用于基因组方面的SSR挖掘和统计的新工具。它比现有的工具SSR Locator和MISA更快、更准确。如果DNA序列太长，则在几个Mb处将其分块成短片段，然后使用Perl强大的模式匹配功能生成基序并进行搜索。然后将来自每个区块的匹配的基因座数据合并，以产生最终的SSR基因座信息。只需要一个包含原始FASTA DNA序列的输入文件，并以表格格式输出文件，列出所有SSR基因座信息和四个分类的统计分布。GMATo是用Java和Perl编写的，既有图形界面，也有命令行界面，两者都可以以独立于平台的方式单独执行，并完全控制参数。GMATo软件是一个强大的工具，可以在任何大小的基因组中进行完整的SSR表征。软GMATO可在http://sourceforge.net/projects/gmato/files/?source=navbar上免费获得，或通过联系获得
Simple Sequence Repeats (SSR), also called microsatellite, is very useful for genetic marker development and genome application. The increasing whole sequences of more and more large genomes provide sources for SSR mining in silico. However currently existing SSR mining tools can’t process large genomes efficiently and generate no or poor statistics. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel tool for SSR mining and statistics at genome aspects. It is faster and more accurate than existed tools SSR Locator and MISA. If a DNA sequence was too long, it was chunked to short segments at several Mb followed by motifs generation and searching using Perl powerful pattern match function. Matched loci data from each chunk were then merged to produce final SSR loci information. Only one input file is required which contains raw fasta DNA sequences and output files in tabular format list all SSR loci information and statistical distribution at four classifications. GMATo was programmed in Java and Perl with both graphic and command line interface, either executable alone in platform independent manner with full parameters control. Software GMATo is a powerful tool for complete SSR characterization in genomes at any size. The soft GMATo is freely available at http://sourceforge.net/projects/gmato/files/?source=navbar or on contact