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Nucleic Acids Research 2006 34(Web Server issue):W656-W659; doi:10.1093/nar/gkl083
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

Erica Jewell1,2, Andrew Robinson1,2, David Savage1, Tim Erwin1,2, Christopher G. Love1,2, Geraldine A. C. Lim1,2, Xi Li1, Jacqueline Batley1, German C. Spangenberg1,2,3 and David Edwards1,2,3,*

1 Department of Primary Industries, Plant Biotechnology Centre, Primary Industries Research Victoria, Victorian AgriBiosciences Centre 1 Park Drive, Bundoora, Victoria 3083, Australia 2 Department of Primary Industries, Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, Victorian AgriBiosciences Centre 1 Park Drive, Bundoora, Victoria 3083, Australia 3 Department of Primary Industries, Australian Centre for Plant Functional Genomics, Plant Biotechnology Centre, Primary Industries Research Victoria, Victorian AgriBiosciences Centre 1 Park Drive, Bundoora, Victoria 3083, Australia

*To whom correspondence should be addressed. Tel: +61 0 3 94795633; Fax: +61 0 3 94793618; Email: Dave.Edwards{at}dpi.vic.gov.au

Received February 13, 2006. Accepted March 6, 2006.

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.


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