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Genomics Inform > Volume 9(4); 2011 > Article
SSR-Primer Generator: A Tool for Finding Simple Sequence Repeats and Designing SSR-Primers.
Chang Pyo Hong, Su Ryun Choi, Yong Pyo Lim
1Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 305-764, Korea. yplim@cnu.ac.kr
2Division of Molecular & Life Sciences, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Korea.
Abstract
Simple sequence repeats (SSRs) are ubiquitous short tandem duplications found within eukaryotic genomes. Their length variability and abundance throughout the genome has led them to be widely used as molecular markers for crop-breeding programs, facilitating the use of marker-assisted selection as well as estimation of genetic population structure. Here, we report a software application, "SSR-Primer Generator" for SSR discovery, SSR-primer design, and homology-based search of in silico amplicons from a DNA sequence dataset. On submission of multiple FASTA-format DNA sequences, those analyses are batch processed in a Java runtime environment (JRE) platform, in a pipeline, and the resulting data are visualized in HTML tabular format. This application will be a useful tool for reducing the time and costs associated with the development and application of SSR markers.
Keywords: EST clustering and assembly; homology-based search; in silico amplicon; PCR; simple sequence repeat (SSR); SSR-primer
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