Optimal sequence alignment using affine gap costs.

  title={Optimal sequence alignment using affine gap costs.},
  author={Stephen F. Altschul and Bruce W. Erickson},
  journal={Bulletin of mathematical biology},
  volume={48 5-6},
When comparing two biological sequences, it is often desirable for a gap to be assigned a cost not directly proportional to its length. If affine gap costs are employed, in other words if opening a gap costs v and each null in the gap costs u, the algorithm of Gotoh (1982, J. molec. Biol. 162,705) finds the minimum cost of aligning two sequences in order MN steps. Gotoh’s algorithm attempts to find only one from among possibly many optimal (minimum-cost) alignments, but does not always succeed… CONTINUE READING