Space-efficient approximate string matching allowing inversions in fast average time

Hwee Kim; Yo Sub Han

doi:10.1007/978-3-319-08016-1_13

Space-efficient approximate string matching allowing inversions in fast average time

Hwee Kim, Yo Sub Han

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

An inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. We investigate the string matching problem allowing inversions: Given a pattern P and a text T, find all indices of matching substrings of T when non-overlapping inversions are allowed. We design an O(nm) algorithm using O(m) space, where n is the size of T and m is the size of P. The proposed algorithm improves the space complexity of the best-known algorithm, which runs in O(nm) time with O(m ²) space. We, furthermore, improve the algorithm and achieve O(max{n, min{nm,nm 5-t/2 }}) average runtime for an alphabet of size t, which is faster than O(nm) when t ≥ 4.

Original language	English
Title of host publication	Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings
Publisher	Springer Verlag
Pages	141-150
Number of pages	10
ISBN (Print)	9783319080154
DOIs	https://doi.org/10.1007/978-3-319-08016-1_13
Publication status	Published - 2014 Jan 1
Event	8th International Frontiers of Algorithmics Workshop, FAW 2014 - Zhangjiajie, China Duration: 2014 Jun 28 → 2014 Jun 30

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	8497 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	8th International Frontiers of Algorithmics Workshop, FAW 2014
Country	China
City	Zhangjiajie
Period	14/6/28 → 14/6/30

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-319-08016-1_13

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Kim, H., & Han, Y. S. (2014). Space-efficient approximate string matching allowing inversions in fast average time. In Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings (pp. 141-150). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8497 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-08016-1_13

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Kim, H & Han, YS 2014, Space-efficient approximate string matching allowing inversions in fast average time. in Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8497 LNCS, Springer Verlag, pp. 141-150, 8th International Frontiers of Algorithmics Workshop, FAW 2014, Zhangjiajie, China, 14/6/28. https://doi.org/10.1007/978-3-319-08016-1_13

Space-efficient approximate string matching allowing inversions in fast average time. / Kim, Hwee; Han, Yo Sub.

Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings. Springer Verlag, 2014. p. 141-150 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8497 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Kim H, Han YS. Space-efficient approximate string matching allowing inversions in fast average time. In Frontiers in Algorithmics - 8th International Workshop, FAW 2014, Proceedings. Springer Verlag. 2014. p. 141-150. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-08016-1_13