GenoFrag

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Software to design primers optimized for whole genome scanning by long-range PCR amplification

N. Ben Zakour, M. Gautier, R. Andonov, D. Lavenier, M-F. Cochet, P. Veber, A. Sorokin, Y. Le Loir
Nucleic Acids Research, 32 (1) 2004 (link)

Abstract: Genome sequence data can be used for the analysis of the genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be entirely amplified by long range PCR using a set of primers designed from a reference strain and used on several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we 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 by long range PCR in ~10 kb-long fragments.

Dynamic programming for LR-PCR segmention of bacterium genomes

R. Andonov, D. Lavenier, P. Veber, N. Yanev
HiComb 2004: Third IEEE International Workshop on High Performance Computational Biology, Santa Fe, New Mexico, USA, 2004 (pdf)

Abstract: Bacterium genome plasticity can efficiently be studied by Long-Range PCR: genomes of different strains are split into hundreds of short segments which, after LR-PCR amplification, are used to sketch profiles. The segments have (1) to cover the entire genome, (2) to overlap each other, and (3) to be of nearly identical size. This paper adresses the problem of finding the optimal list of segments satisfying these constraints. Two approaches using dynamic programming are presented. They differ on the optimization criteria for measuring the quality of the covering. One considers the maximal deviation of the segment lengths relatively to a ideal length. The other automatically find a segment length which minimizes the maximal deviation.