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.
authors.affiliation: Department of Primary Industries, Plant Biotechnology Centre, Primary Industries Research Victoria, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora, Victoria 3083, Australia.
authors.forename: Erica
authors.initials: E
authors.lastname: Jewell
authors.forename: Andrew
authors.initials: A
authors.lastname: Robinson
authors.forename: David
authors.initials: D
authors.lastname: Savage
authors.forename: Tim
authors.initials: T
authors.lastname: Erwin
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Love
authors.forename: Geraldine A C
authors.initials: GA
authors.lastname: Lim
authors.forename: Xi
authors.initials: X
authors.lastname: Li
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.forename: German C
authors.initials: GC
authors.lastname: Spangenberg
authors.forename: David
authors.initials: D
authors.lastname: Edwards
mesh_terms: D002965:Classification; D017931:DNA Primers; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D020407:Internet; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers; D005819:Genetic Markers