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《Molecular Plant Breeding》 2015-01
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Comparison of Different Search Tools to Find Microsatellite Sites in Unigene Sequences of Salix babylonica

He Xudong;Zheng Jiwei;He Kaiyue;Wang Baosong;Jiangsu Academy of Forestry;College of Forest Resources and Environment, Nanjing Forestry University;  
What kind of search to ols 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.
【Fund】: 江苏省自然科学基金(BK2011871);; 国家自然科学基金(31300556)共同资助
【CateGory Index】: S792.12
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