A space efficient algorithm for sequence alignment with inversions

Authors:
Yong Gao;Junfeng Wu;Robert Niewiadomski;Yang Wang;Zhi-Zhong Chen;Guohui Lin
Affiliations:
Computing Science, University of Alberta, Edmonton, Alberta, Canada;Computing Science, University of Alberta, Edmonton, Alberta, Canada;Computing Science, University of Alberta, Edmonton, Alberta, Canada;Computing Science, University of Alberta, Edmonton, Alberta, Canada;Mathematical Sciences, Tokyo Denki Univ., Hatoyama, Saitama, Japan;Computing Science, University of Alberta, Edmonton, Alberta, Canada
Venue:
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Year:
2003

Citing 2
Cited 1

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Algorithms on strings, trees, and sequences: computer science and computational biology
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LATIN '02 Proceedings of the 5th Latin American Symposium on Theoretical Informatics

Alignment with non-overlapping inversions in O(n3)-time

WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics

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Abstract

A dynamic programming algorithm to find an optimal alignment for a pair of DNA sequences has been described by Schöniger and Waterman. The alignments use not only substitutions, insertions, and deletions of single nucleotides, but also inversions, which are the reversed complements, of substrings of the sequences. With the restriction that the inversions are pairwise non-intersecting, their proposed algorithm runs in O(n2m2) time and consumes O(n2m2) space, where n and m are the lengths of the input sequences respectively. We develop a space efficient algorithm to compute such an optimal alignment which consumes only O(nm) space within the same amount of time. Our algorithm enables the computation for a pair of DNA sequences of length up to 10,000 to be carried out on an ordinary desktop computer. Simulation study is conducted to verify some biological facts about gene shuffling across species.