Efficient matching of biological sequences allowing for non-overlapping inversions

Authors:
Domenico Cantone;Salvatore Cristofaro;Simone Faro
Affiliations:
Università degli Studi di Catania, Dipartimento di Matematica e Informatica, Catania, Italy;Università degli Studi di Catania, Dipartimento di Matematica e Informatica, Catania, Italy;Università degli Studi di Catania, Dipartimento di Matematica e Informatica, Catania, Italy
Venue:
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Year:
2011

Citing 5
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Abstract

Inversions are a class of chromosomal mutations, widely regarded as one of the major mechanisms for reorganizing the genome. In this paper we present a new algorithm for the approximate string matching problem allowing for non-overlapping inversions which runs in O(nm) worst-case time and O(m2)-space, for a character sequence of size n and pattern of size m. This improves upon a previous O(nm2)-time algorithm.