title: GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.
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.
authors.affiliation: 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.
authors.forename: Nouri
authors.initials: N
authors.lastname: Ben Zakour
authors.forename: Michel
authors.initials: M
authors.lastname: Gautier
authors.forename: Rumen
authors.initials: R
authors.lastname: Andonov
authors.forename: Dominique
authors.initials: D
authors.lastname: Lavenier
authors.forename: Marie-Françoise
authors.initials: MF
authors.lastname: Cochet
authors.forename: Philippe
authors.initials: P
authors.lastname: Veber
authors.forename: Alexei
authors.initials: A
authors.lastname: Sorokin
authors.forename: Yves
authors.initials: Y
authors.lastname: Le Loir
mesh_terms: D020029:Base Pairing; D002876:Chromosomes, Bacterial / Q000235:genetics; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics*; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D012984:Software; D013211:Staphylococcus aureus / Q000145:classification / Q000235:genetics; D013816:Thermodynamics
chemical_list: D017931:DNA Primers