| Title | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. |
| Publication Type | Journal Article |
| Year of Publication | 2008 |
| Authors | Yao, J, Lin, H, Van Deynze, A, Doddapaneni, H, Francis, M, Lemos, EGertrudes, Civerolo, EL |
| Journal | BMC Microbiol |
| Volume | 8 |
| Pagination | 185 |
| Date Published | 2008 Oct 20 |
| ISSN | 1471-2180 |
| Keywords | Alleles, 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.
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| DOI | 10.1186/1471-2180-8-185 |
| Alternate Journal | BMC Microbiol |
| PubMed ID | 18937861 |
| PubMed Central ID | PMC2579435 |