不同检索工具检索垂柳Unigene序列SSR位点的效率比较

Comparison of Different Search Tools to Find Microsatellite Sites in Unigene Sequences of Salix babylonica

在SSR标记开发中,合适的位点检索工具是获取位点信息、保障位点准确度及提高开发效率的关键。本研究选取了国内外文献中常用的11种基于Windows系统或在线形式的检索工具对垂柳Unigene序列进行SSR位点检索,比较了不同检索工具的参数设置、使用方式、数据录入量、运行时间、位点统计信息量及位点准确度。经综合对比,检索工具MISA位点检出率及准确度最高,结果统计信息最为丰富;检索工具SSR Locator位点检出率比MISA略低,但操作相对简单,运行时间短,且能对候选位点进行引物设计并模拟PCR反应。因此,推荐MISA和SSR Locator为微卫星位点检索的首选工具。

What kind of search tools we choose is very critical for mining microsatellite with plenty of locus information and locus accuracy as well as high developmental efficiency. In present study, eleven search tools based on Windows operation system or online running were employed to compare their parameter setting-up, operational patterns, data availability, running time, locus information and accuracy through screening the SSR loci in the unigenes of S. babylonica. With the comprehensive comparison, MISA was proved to be the most efficient due to the highest accuracy and the most informative. While SSR Locator with the advantages of easier operating and shorter running time as well as easy for primer designing and PCR simulating for candidate locus was also an ideal alternative to MISA although the detection rate was slightly lower than MISA. Therefore, MISA and SSR Locator are preferentially recommended for mining microsatellite loci in this study.