Alignment with non-overlapping inversions on two strings

Da Jung Cho, Yo Sub Han, Hwee Kim

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish
Title of host publicationAlgorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings
PublisherSpringer Verlag
Pages261-272
Number of pages12
Volume8344 LNCS
ISBN (Print)9783319046563
DOIs
Publication statusPublished - 2014 Jan 1
Event8th International Workshop on Algorithms and Computation, WALCOM 2014 - Chennai, India
Duration: 2014 Feb 132014 Feb 15

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8344 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other8th International Workshop on Algorithms and Computation, WALCOM 2014
CountryIndia
CityChennai
Period14/2/1314/2/15

Fingerprint

Inversion
Alignment
Strings
Efficient Algorithms
Sequence Comparison
Sequence Alignment
Sequence Analysis

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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 (Vol. 8344 LNCS, 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
Cho, Da Jung ; Han, Yo Sub ; Kim, Hwee. / Alignment with non-overlapping inversions on two strings. Algorithms and Computation - 8th International Workshop, WALCOM 2014, Proceedings. Vol. 8344 LNCS Springer Verlag, 2014. pp. 261-272 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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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. vol. 8344 LNCS, 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. Vol. 8344 LNCS 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 proceedingConference 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. Vol. 8344 LNCS. 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