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BMC Research Notes

, 4:146

First Online: 23 May 2011Received: 09 December 2010Accepted: 23 May 2011DOI: 10.1186-1756-0500-4-146

Cite this article as: Seroussi, Y., Shirak, A. & Seroussi, E. BMC Res Notes 2011 4: 146. doi:10.1186-1756-0500-4-146

Abstract

BackgroundBeef 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.

FindingsTo 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.

ConclusionsModified 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.

List of abbreviationsCGIcommon gateway interface

SNPsingle nucleotide polymorphism

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-4-146 contains supplementary material, which is available to authorized users.

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Author: Yanir Seroussi - Andrey Shirak - Eyal Seroussi

Source: https://link.springer.com/



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