Microsatellites, also known as simple sequence repeats (SSRs), are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. We have created a software tool, AutoSSR, for quickly detecting simple sequence repeats from a large number of sequences. The software can detect SSRs from one file, including large number of FASTA-formatted sequences, and analyze the distributions of different SSR types. Importantly, this tool is not restricted to sequence numbers and different system platforms with high efficiency and vast amounts of information. We have applied this tool for the discovery of SSRs within DNA sequences publicly released in GenBank in Gossypium, Malus Pumila and Oryza sativa L., in which we detected over 36000 SSRs. Of the identified SSRs, we parsed information Gossypium to Primer 3 software for designing locus-specific primers and applications in genomics analysis.%为从大量的序列中快速发掘和利用简单序列重复(微卫星,SSRs),开发了一个软件工具--AutoSSR.该软件能够从一个包括大量FASTA格式的序列文件中发掘SSR,并分析不同SSRs类型的分布状况.与已开发的类似软件相比,该软件可以不受序列数量和不同系统平台的限制,高效、快速完成SSR信息的搜索和分析.利用该软件对GenBank上释放的来源于棉花、苹果和水稻的DNA序列进行了SSR发掘,得到了36000个SSRs.其中,对来源于棉花的SSRs信息,进一步利用Primer 3软件开发了位点特异性引物,为棉花基因组分析奠定了基础.
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