Alignment with non-overlapping inversions on two strings

Da Jung Cho; Yo Sub Han; Hwee Kim

doi:10.1007/978-3-319-04657-0_25

Alignment with non-overlapping inversions on two strings

Da Jung Cho, Yo Sub Han, Hwee Kim

Department of Computer Science

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

6 Citations (Scopus)

Abstract

The inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. Based on inversion operations, we introduce the alignment with non-overlapping inversion problem: Given two strings x and y, does there exist an alignment with non-overlapping inversions for x and y. We, in particular, consider the alignment problem when non-overlapping inversions are allowed for both x and y. We design an efficient algorithm that determines the existence of non-overlapping inversions and present another efficient algorithm that retrieves such an alignment, if exists.

Original language	English
Title of host publication	Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings
Publisher	Springer Verlag
Pages	261-272
Number of pages	12
ISBN (Print)	9783319046563
DOIs	https://doi.org/10.1007/978-3-319-04657-0_25
Publication status	Published - 2014
Event	8th International Workshop on Algorithms and Computation, WALCOM 2014 - Chennai, India Duration: 2014 Feb 13 → 2014 Feb 15

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	8344 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	8th International Workshop on Algorithms and Computation, WALCOM 2014
Country	India
City	Chennai
Period	14/2/13 → 14/2/15

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-319-04657-0_25

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Cho, D. J., Han, Y. S., & Kim, H. (2014). Alignment with non-overlapping inversions on two strings. In Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings (pp. 261-272). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8344 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-04657-0_25

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abstract = "The inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. Based on inversion operations, we introduce the alignment with non-overlapping inversion problem: Given two strings x and y, does there exist an alignment with non-overlapping inversions for x and y. We, in particular, consider the alignment problem when non-overlapping inversions are allowed for both x and y. We design an efficient algorithm that determines the existence of non-overlapping inversions and present another efficient algorithm that retrieves such an alignment, if exists.",

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Cho, DJ, Han, YS & Kim, H 2014, Alignment with non-overlapping inversions on two strings. in Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8344 LNCS, Springer Verlag, pp. 261-272, 8th International Workshop on Algorithms and Computation, WALCOM 2014, Chennai, India, 14/2/13. https://doi.org/10.1007/978-3-319-04657-0_25

Alignment with non-overlapping inversions on two strings. / Cho, Da Jung; Han, Yo Sub; Kim, Hwee.

Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings. Springer Verlag, 2014. p. 261-272 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8344 LNCS).

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

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AB - The inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. Based on inversion operations, we introduce the alignment with non-overlapping inversion problem: Given two strings x and y, does there exist an alignment with non-overlapping inversions for x and y. We, in particular, consider the alignment problem when non-overlapping inversions are allowed for both x and y. We design an efficient algorithm that determines the existence of non-overlapping inversions and present another efficient algorithm that retrieves such an alignment, if exists.

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Cho DJ, Han YS, Kim H. Alignment with non-overlapping inversions on two strings. In Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings. Springer Verlag. 2014. p. 261-272. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-04657-0_25

Alignment with non-overlapping inversions on two strings

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