GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Nouri Ben Zakour 1 Michel Gautier 1 Rumen Andonov 2 Dominique Lavenier 2 Marie-Françoise Cochet 1 Philippe Veber 2 Alexei Sorokine 3 Yves Le Loir 1
1 STLO - Science et Technologie du Lait et de l'Oeuf
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
3 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé humaine
Abstract : Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.
Keywords : génome séquençage PCR caractérisation de souche bactérienne genofrag
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Journal articles
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Submitted on : Thursday, February 2, 2017 - 9:25:38 PM
Last modification on : Friday, November 16, 2018 - 1:23:09 AM

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INRA | UNAM | IRISA | AGROCAMPUS-OUEST | AGROPARISTECH | UR1-UFR-ISTIC | UNIV-RENNES1 | INRIA | UNIV-RENNES | INSA-GROUPE

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Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Marie-Françoise Cochet, et al.. GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.. Nucleic Acids Research, Oxford University Press, 2004, 32 (1), pp.17-24. ⟨10.1093/nar/gkg928⟩. ⟨hal-01454461⟩

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