Inverse Parametric Sequence Alignment

Authors:
Fangting Sun;David Fernández-Baca;Wei Yu
Affiliations:
-;-;-
Venue:
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
Year:
2002

Citing 4
Cited 1

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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(mn logm) 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.