Paper Info
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.
Year
DOI
Venue
2006
10.1093/nar/gkl083
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
genomes,evolution,genome mapping,classification,dna sequence,simple sequence repeats,internet,dna markers,molecular genetics,genetic markers,genetic diversity,abundance,dna primers,microsatellites,polymerase chain reaction
Genome,Genetic diversity,Biology,Microsatellite,Gene mapping,DNA sequencing,Locus (genetics),Genetics,Molecular biology,GenBank,Genetic marker
Journal
Volume
Issue
ISSN
34
Web Server issue
0305-1048
Citations 
PageRank 
References 
6
1.67
0
Authors
10
Name
Order
Citations
PageRank
Erica Jewell161.67
Andrew Robinson283.07
David Savage3232.95
Tim Erwin4142.95
Christopher G Love5163.67
Geraldine A C Lim6163.67
Xi Li772.18
Jacqueline Batley8437.58
German C Spangenberg9164.01
David Edwards1063.03