Inverse parametric sequence alignment

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(mn logn)-time algorithm for inverse global alignment without gap penalties and a O(mn login) time algorithm for global alignment with gap penalties, where m, n (n[Less than or equal to symbol]m) are the lengths of input strings. Finally, we discuss the local alignment problem and future work