Inverse parametric sequence alignment

Abstract

We consider the inverse parametric sequence alignment problem, where a sequence alignment is given and the task is to determine parameter values such that the given alignment is optimal at that parameter setting. We describe a O(mnlog n)-time algorithm for inverse global alignment without gap penalty and a O(mnlogm) time algorithm for global alignment with gap penalty, where m, n (n ≤ m) are the lengths of input strings. We then discuss algorithms for local alignment.