Dynamic programming for LR-PCR segmention of bacterium genomes

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 a list of segments satisfying these constraints “as much as possible”. Two algorithmes 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.

Dynamic programming for LR-PCR segmention of bacterium genomes

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 a list of segments satisfying these constraints "as much as possible". Two algorithmes 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