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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth104
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 6, 2003
Revised August 10, 2003
Accepted December 17, 2003

Applications note

Simple sequence repeat marker loci discovery using SSR primer

Andrew J. Robinson 1, Christopher G. Love 1, Jacqueline Batley 2, Gary Barker 3, David Edwards 1*

1 Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Bundoora 3086, Victoria, Australia; Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Bundoora 3086, Victoria, Australia
2 Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Bundoora 3086, Victoria, Australia
3 School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK

* To whom correspondence should be addressed. E-mail: Dave.Edwards{at}dpi.vic.gov.au.


  Abstract

Summary: SSRs (Single Sequence Repeats) have become important molecular markers for a broad range of applications such as genome mapping and characterisation, phenotype mapping, marker assisted selection of crop plants as well as 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 the 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. 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/.


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