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Inverse Parametric Sequence Alignment
 In: International Computing and Combinatorics Conference (COCOON). (2002
, 2002
"... 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(rnn log m)time algorithm for inverse global alignment without gaps ..."
Abstract

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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(rnn log m)time algorithm for inverse global alignment without gaps and a O(rnn log 2 rn) time algorithm for global alignment with gaps, where rn, ( _ rn) are the lengths of input strings. We then discuss algorithms for local alignment.