PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.

TitlePrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.
Publication TypeJournal Article
Year of Publication2008
AuthorsYao, J, Lin, H, Van Deynze, A, Doddapaneni, HV, Francis, M, Lemos, EGertrudes, Civerolo, EL
JournalBMC Microbiol
Volume8
Pagination185
Date Published2008 Oct 20
ISSN1471-2180
KeywordsAlleles, Bacteria, Computational Biology, DNA Primers, Genome, Bacterial, Internet, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Sequence Alignment, Software
Abstract

BACKGROUND: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.RESULTS: PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/~primer.CONCLUSION: PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.

DOI10.1186/1471-2180-8-185
Alternate JournalBMC Microbiol.
PubMed ID18937861
PubMed Central IDPMC2579435