Computational experiments with multicriteria sequence alignment

Authors

Abstract

In this article we investigate the performance of multicriteria dynamic programming algorithm for pairwise sequence alignment that maximizes the number of matches and minimizes the number of indels or/and gaps. We give explicit recurrence relations for a number of multicriteria score functions. In addition, we provide estimates on the number of optimal alignments for pairs of random sequences, as well as computational results in two benchmark datasets.