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

dc.contributorUniversidade Estadual Paulista (UNESP)
dc.creatorYao, Jiqiang
dc.creatorLin, Hong
dc.creatorVan Deynze, Allen
dc.creatorDoddapaneni, Harshavardhan
dc.creatorFrancis, Martha
dc.creatorMacedo Lemos, Eliana Gertrudes
dc.creatorCiverolo, Edwin L.
dc.date2014-05-20T15:33:55Z
dc.date2016-10-25T18:10:34Z
dc.date2014-05-20T15:33:55Z
dc.date2016-10-25T18:10:34Z
dc.date2008-10-20
dc.date.accessioned2017-04-06T00:35:10Z
dc.date.available2017-04-06T00:35:10Z
dc.identifierBmc Microbiology. London: Biomed Central Ltd., v. 8, p. 9, 2008.
dc.identifier1471-2180
dc.identifierhttp://hdl.handle.net/11449/42359
dc.identifierhttp://acervodigital.unesp.br/handle/11449/42359
dc.identifier10.1186/1471-2180-8-185
dc.identifierWOS:000260747900001
dc.identifierWOS000260747900001.pdf
dc.identifierhttp://dx.doi.org/10.1186/1471-2180-8-185
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/885011
dc.descriptionBackground: 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/similar to 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.
dc.languageeng
dc.publisherBiomed Central Ltd.
dc.relationBMC Microbiology
dc.rightsinfo:eu-repo/semantics/openAccess
dc.titlePrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences
dc.typeOtro


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