PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences
<p>Abstract</p> <p>Background</p> <p>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 genomi...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-10-01
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| Series: | BMC Microbiology |
| Online Access: | http://www.biomedcentral.com/1471-2180/8/185 |
| _version_ | 1819203119065595904 |
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| author | Lemos Eliana Francis Martha Doddapaneni Harshavardhan Lin Hong Van Deynze Allen Yao Jiqiang Civerolo Edwin L |
| author_facet | Lemos Eliana Francis Martha Doddapaneni Harshavardhan Lin Hong Van Deynze Allen Yao Jiqiang Civerolo Edwin L |
| author_sort | Lemos Eliana |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <url>http://cropdisease.ars.usda.gov/~primer</url>.</p> <p>Conclusion</p> <p>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.</p> |
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| format | Article |
| id | doaj.art-b180b568483f4f4cba1e4c0b615ca8c5 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-23T04:14:50Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-b180b568483f4f4cba1e4c0b615ca8c52022-12-21T18:00:23ZengBMCBMC Microbiology1471-21802008-10-018118510.1186/1471-2180-8-185PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequencesLemos ElianaFrancis MarthaDoddapaneni HarshavardhanLin HongVan Deynze AllenYao JiqiangCiverolo Edwin L<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <url>http://cropdisease.ars.usda.gov/~primer</url>.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2180/8/185 |
| spellingShingle | Lemos Eliana Francis Martha Doddapaneni Harshavardhan Lin Hong Van Deynze Allen Yao Jiqiang Civerolo Edwin L PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences BMC Microbiology |
| title | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences |
| title_full | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences |
| title_fullStr | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences |
| title_full_unstemmed | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences |
| title_short | PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences |
| title_sort | primersnp a web tool for whole genome selection of allele specific and common primers of phylogenetically related bacterial genomic sequences |
| url | http://www.biomedcentral.com/1471-2180/8/185 |
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