Dynamic programming for LR-PCR segmentation of bacterium genomes

Summary form only given. 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. We address the problem of finding a list of segments satisfying these constraints "as much as possible". Two algorithms based on dynamic programming approach are presented. They differ on the optimization criteria for measuring the quality of the covering. The first one considers the maximal deviation of the segment lengths relatively to an ideal length. The second one automatically finds a segment length which minimizes the maximal deviation.