Simple sequence repeat marker loci discovery using SSR primer

AJ Robinson, CG Love, Jacqueline Batley, G Barker, D Edwards

    Research output: Contribution to journalArticle

    85 Citations (Scopus)

    Abstract

    Summary: Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use.

    Availability: This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/
    Original languageEnglish
    Pages (from-to)1475-1476
    JournalBioinformatics
    Volume20
    Issue number9
    DOIs
    Publication statusPublished - 2004

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