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Published online 2 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 17-24
© 2004 Oxford University Press

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

Nouri Ben Zakour, Michel Gautier, Rumen Andonov1, Dominique Lavenier1, Marie-Françoise Cochet, Philippe Veber1, Alexei Sorokin2 and Yves Le Loir*

Laboratoire d’Hygiène Alimentaire, UMR STLO, Institut National de la Recherche Agronomique, Ecole Nationale Supérieure Agronomique, 65 rue de Saint Brieuc, CS84215, 35042 Rennes cedex, France, 1 Institut de Recherche en Informatique et Systèmes Aléatoires, Campus Universitaire de Beaulieu, 35042 Rennes cedex, France and 2 Unité de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas cedex, France

*To whom correspondence should be addressed. Tel: +33 2 23 48 59 04; Fax: +33 2 23 48 59 02; Email: leloir{at}roazhon.inra.fr

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 ~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.


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