Table of Contents
International Journal of Plant Genomics
Volume 2008 (2008), Article ID 412696, 9 pages
http://dx.doi.org/10.1155/2008/412696
Resource Review

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

1Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
2Laboratory for Environmental Studies, Catholic University of Salvador, Salvador, BA, 40.220-140, Brazil

Received 5 October 2007; Revised 29 January 2008; Accepted 20 May 2008

Academic Editor: Chunguang Du

Copyright © 2008 Luciano Carlos da Maia et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.