SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

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 f...

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Main Authors:	Jewell, Erica, Robinson, Andrew, Savage, David, Erwin, Tim, Love, Christopher G., Lim, Geraldine A. C., Li, Xi, Batley, Jacqueline, Spangenberg, German C., Edwards, David
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538772/

id	pubmed-1538772
recordtype	oai_dc
spelling	pubmed-15387722006-08-18 SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery Jewell, Erica Robinson, Andrew Savage, David Erwin, Tim Love, Christopher G. Lim, Geraldine A. C. Li, Xi Batley, Jacqueline Spangenberg, German C. Edwards, David Article 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 . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538772/ /pubmed/16845092 http://dx.doi.org/10.1093/nar/gkl083 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Jewell, Erica Robinson, Andrew Savage, David Erwin, Tim Love, Christopher G. Lim, Geraldine A. C. Li, Xi Batley, Jacqueline Spangenberg, German C. Edwards, David
spellingShingle	Jewell, Erica Robinson, Andrew Savage, David Erwin, Tim Love, Christopher G. Lim, Geraldine A. C. Li, Xi Batley, Jacqueline Spangenberg, German C. Edwards, David SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
author_facet	Jewell, Erica Robinson, Andrew Savage, David Erwin, Tim Love, Christopher G. Lim, Geraldine A. C. Li, Xi Batley, Jacqueline Spangenberg, German C. Edwards, David
author_sort	Jewell, Erica
title	SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
title_short	SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
title_full	SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
title_fullStr	SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
title_full_unstemmed	SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
title_sort	ssrprimer and ssr taxonomy tree: biome ssr discovery
description	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 .
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538772/
_version_	1611386381587709952

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

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