ÃÞ »¨ ѧ ±¨       Cotton Science     2009£¬21(3)£º243-247

 

 

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
(1.State Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095£¬China; 2.Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, Shanxi 044000, China; 3.Shanxi Academy of Agricultural Sciences, Taiyuan 030006, China)

Abstract£ºMicrosatellites, 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.
Key words£ºsimple sequence repeats; expressed sequence tags; distribution; software
CLC£ºS562         Document Code£ºA
Article ID£º1002-7807£¨2009£©03-0243-05    [Full Text, 1969KB]