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

7 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/Territory	India
City	Chennai
Period	14/2/13 → 14/2/15

Bibliographical note

Funding Information:
This research was supported by the Basic Science Research Program through NRF funded by MEST (2012R1A1A2044562).

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

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

Cite this

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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note = "Funding Information: This research was supported by the Basic Science Research Program through NRF funded by MEST (2012R1A1A2044562).; 8th International Workshop on Algorithms and Computation, WALCOM 2014 ; Conference date: 13-02-2014 Through 15-02-2014",

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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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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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