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SNPmplexViewer--toward a cost-effective traceability system
BACKGROUND: Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using SNaP...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120698/ https://www.ncbi.nlm.nih.gov/pubmed/21600063 http://dx.doi.org/10.1186/1756-0500-4-146 |
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author | Seroussi, Yanir Shirak, Andrey Seroussi, Eyal |
author_facet | Seroussi, Yanir Shirak, Andrey Seroussi, Eyal |
author_sort | Seroussi, Yanir |
collection | PubMed |
description | BACKGROUND: Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using SNaPshot, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control. FINDINGS: To further decrease SNaPshot's cost, we introduced the Perl script SNPmplexViewer, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. SNPmplexViewer automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. SNPmplexViewer produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. SNPmplexViewer also outputs aligned images of the two electropherograms together with a difference profile. CONCLUSIONS: Modified trace files generated by SNPmplexViewer enable genotyping of SnaPshot reactions performed without fluorescent size standards, using common fragment-sizing software packages. SNPmplexViewer's normalised output may also improve the genotyping software's performance. Thus, SNPmplexViewer is a general free tool enabling the reduction of SNaPshot's cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. SNPmplexViewer is available at http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi. |
format | Online Article Text |
id | pubmed-3120698 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31206982011-06-23 SNPmplexViewer--toward a cost-effective traceability system Seroussi, Yanir Shirak, Andrey Seroussi, Eyal BMC Res Notes Research Article BACKGROUND: Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using SNaPshot, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control. FINDINGS: To further decrease SNaPshot's cost, we introduced the Perl script SNPmplexViewer, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. SNPmplexViewer automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. SNPmplexViewer produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. SNPmplexViewer also outputs aligned images of the two electropherograms together with a difference profile. CONCLUSIONS: Modified trace files generated by SNPmplexViewer enable genotyping of SnaPshot reactions performed without fluorescent size standards, using common fragment-sizing software packages. SNPmplexViewer's normalised output may also improve the genotyping software's performance. Thus, SNPmplexViewer is a general free tool enabling the reduction of SNaPshot's cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. SNPmplexViewer is available at http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi. BioMed Central 2011-05-23 /pmc/articles/PMC3120698/ /pubmed/21600063 http://dx.doi.org/10.1186/1756-0500-4-146 Text en Copyright ©2011 Seroussi et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Seroussi, Yanir Shirak, Andrey Seroussi, Eyal SNPmplexViewer--toward a cost-effective traceability system |
title | SNPmplexViewer--toward a cost-effective traceability system |
title_full | SNPmplexViewer--toward a cost-effective traceability system |
title_fullStr | SNPmplexViewer--toward a cost-effective traceability system |
title_full_unstemmed | SNPmplexViewer--toward a cost-effective traceability system |
title_short | SNPmplexViewer--toward a cost-effective traceability system |
title_sort | snpmplexviewer--toward a cost-effective traceability system |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120698/ https://www.ncbi.nlm.nih.gov/pubmed/21600063 http://dx.doi.org/10.1186/1756-0500-4-146 |
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