Inverse parametric sequence alignment

Authors:
Fangting Sun;David Fernández-Baca;Wei Yu
Affiliations:
Department of Computer Science, Iowa State University, Ames, IA and Department of Electrical and Computer Engineering, University of Maryland, College Park, MD;Department of Computer Science, Iowa State University, Ames, IA;Department of Computer Science, Washington University, St. Louis, MO and Department of Electrical and Computer Engineering, University of Maryland, College Park, MD
Venue:
Journal of Algorithms
Year:
2004

Citing 8
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Abstract

We consider the inverse parametric sequence alignment problem, where a sequence alignment, called a reference alignment, is given and the task is to determine parameter values such that the reference alignment is optimal for those parameter values. The goal is to produce biologically meaningful alignments, by using reference alignments as a training set. 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 (n ≤ m) are the lengths of input strings. We then discuss algorithms for local alignment and multiple sequence alignment.