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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(mn log n)-time algorithm for inverse global alignment without gap penalty and a O(mn log m) time algorithm for global alignment with gap penalty, where m, n (nm) are the lengths of input strings. We then discuss algorithms for local alignment.
Research partially supported by grant CCR-9988348 from the National Science Foundation.

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