Genomics Inform.  2011 Dec;9(4):189-193.

SSR-Primer Generator: A Tool for Finding Simple Sequence Repeats and Designing SSR-Primers

• Hong CP
• Choi SR
• Lim YP

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.

Keyword

EST clustering and assembly; homology-based search; in silico amplicon; PCR; simple sequence repeat (SSR); SSR-primer

MeSH Terms

Base Sequence
Computer Simulation
Genome
Indonesia
Microsatellite Repeats
Polymerase Chain Reaction