SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

E. Jewell; A. Robinson; D. Savage; T. Erwin; C.G. Love; G.A.C. Lim; X. Li; Jacqueline Batley; G.C. Spangenberg; D. Edwards

doi:10.1093/nar/gkl083

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

E. Jewell, A. Robinson, D. Savage, T. Erwin, C.G. Love, G.A.C. Lim, X. Li, Jacqueline Batley, G.C. Spangenberg, D. Edwards

Research output: Contribution to journal › Article › peer-review

62 Citations (Scopus)

Abstract

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 .

Original language	English
Pages (from-to)	W656-W659
Journal	Nucleic Acids Research
Volume	34
DOIs	https://doi.org/10.1093/nar/gkl083
Publication status	Published - 2006

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10.1093/nar/gkl083Licence: CC BY-NC

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title = "SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery",

abstract = "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 .",

author = "E. Jewell and A. Robinson and D. Savage and T. Erwin and C.G. Love and G.A.C. Lim and X. Li and Jacqueline Batley and G.C. Spangenberg and D. Edwards",

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T1 - SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

AU - Jewell, E.

AU - Robinson, A.

AU - Savage, D.

AU - Erwin, T.

AU - Love, C.G.

AU - Lim, G.A.C.

AU - Li, X.

AU - Batley, Jacqueline

AU - Spangenberg, G.C.

AU - Edwards, D.

PY - 2006

Y1 - 2006

N2 - 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 .

AB - 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 .

U2 - 10.1093/nar/gkl083

DO - 10.1093/nar/gkl083

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VL - 34

SP - W656-W659

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

Abstract

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