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An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome
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SNPmplexViewer--toward a cost-effective traceability system.

Yanir Seroussi1, Andrey Shirak, Eyal Seroussi

  • 1Clayton School of Information Technology, Monash University, Clayton, Victoria 3800, Australia. yanir.seroussi@monash.edu.

BMC Research Notes
|May 24, 2011
PubMed
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SNPmplexViewer, a free Perl script, reduces the cost of DNA-based beef traceability by enabling genotyping without fluorescent size standards. This tool simplifies analyzing DNA trace files for accurate animal identification and product tracking.

Area of Science:

  • Animal genetics
  • Bioinformatics
  • Forensic science

Background:

  • Beef traceability is mandatory globally, often using ear tags and passports.
  • DNA-based traceability offers enhanced accuracy using an animal's unique genetic code.
  • Single Nucleotide Polymorphism (SNP) genotyping is crucial for identity control in traceability systems.

Purpose of the Study:

  • To reduce the cost of SNP genotyping for beef traceability.
  • To develop a method for analyzing DNA trace files without fluorescent size standards.
  • To improve the efficiency of DNA-based animal identification.

Main Methods:

  • Introduction of the Perl script SNPmplexViewer.
  • Analysis of trace files from SNaPshot reactions (a primer-extension method).

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  • Alignment of reference and target electropherograms with and without fluorescent size standards.

    • Main Results:

    • SNPmplexViewer automatically aligns electropherograms and creates normalized trace files.
    • The software embeds reference size standards into target trace files.
    • Output includes aligned electropherogram images and a difference profile for comparison.

    Conclusions:

    • SNPmplexViewer enables genotyping without fluorescent size standards using standard software.
    • The tool potentially improves genotyping software performance through normalized output.
    • SNPmplexViewer is a free tool for cost reduction, fast viewing, and comparing electropherograms in fragment analysis.