A space-efficient algorithm for sequence alignment with inversions and reversals

Authors:
Zhi-Zhong Chen;Yong Gao;Guohui Lin;Robert Niewiadomski;Yang Wang;Junfeng Wu
Affiliations:
Mathematical Sciences, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan;Department of Computing Science, Faculty of Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, Alberta, Canada T6G 2E8;Department of Computing Science, Faculty of Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, Alberta, Canada T6G 2E8;Department of Computing Science, Faculty of Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, Alberta, Canada T6G 2E8;Department of Computing Science, Faculty of Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, Alberta, Canada T6G 2E8;Department of Computing Science, Faculty of Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, Alberta, Canada T6G 2E8
Venue:
Theoretical Computer Science - Special papers from: COCOON 2003
Year:
2004

Citing 2
Cited 3

Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology
An Improved Algorithm for Sequence Comparison with Block Reversals

LATIN '02 Proceedings of the 5th Latin American Symposium on Theoretical Informatics

Efficient matching of biological sequences allowing for non-overlapping inversions

CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Alignments with non-overlapping moves, inversions and tandem duplications in O(n4) time

COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
Efficient string-matching allowing for non-overlapping inversions

Theoretical Computer Science

Quantified Score

Hi-index	0.00

Visualization

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.