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 ampl

SUBMITTER: Ben Zakour N 

PROVIDER: S-EPMC373259 | biostudies-literature | 2004

REPOSITORIES: biostudies-literature