AutoSSR: An Improved Automatic Software for SSR Analysis from Large-scale EST Sequences

WANGChang-Biao, GUOWang-Zhen, ZHANGTian-Zhen, LIYan-E, LIUHui-Min

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Cotton Science ›› 2009, Vol. 21 ›› Issue (3) : 243-247. DOI: 10.11963/cs090315
Article

AutoSSR: An Improved Automatic Software for SSR Analysis from Large-scale EST Sequences

  • WANG Chang-biao1, 2, GUO Wang-zhen1*, ZHANG Tian-zhen1, LI Yan-e2, LIU Hui-min3
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Abstract

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.

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simple sequence repeats

/ expressed sequence tags / distribution / software

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WANGChang-Biao, GUOWang-Zhen, ZHANGTian-Zhen, LIYan-E, LIUHui-Min. AutoSSR: An Improved Automatic Software for SSR Analysis from Large-scale EST Sequences. Cotton Science. 2009, 21(3): 243-247 https://doi.org/10.11963/cs090315

References

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