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

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.

Figure 1

Flow-chart showing the functional structure of SSR Locator. (A) Perl script to search SSRs; (B) text file where information from detected SSRs is stored; (C) module for the statistical calculations for SSR motif occurrence; (D) module that formats text files into standard Primer3 input files; (E) running of Primer3; (F) module for running Virtual-PCR (using a second sequence file as a template); (G) module performing global alignment between homologous amplicons; (H) identity and alignment score calculations between homologous amplicons; and (I) file containing SSR, primer, homologous amplicons, identity, and score information.