skip to main content
10.1145/1854776.1854823acmconferencesArticle/Chapter ViewAbstractPublication PagesbcbConference Proceedingsconference-collections
research-article

An improved 1.375-approximation algorithm for the transposition distance problem

Published: 02 August 2010 Publication History

Abstract

In this work, we deal with transposition events, which are large scale mutational events where a block of genes moves from a region of a chromosome to another region within the same chromosome. The transposition distance is the minimum number of transpositions which transform one genome into another. This problem is still open and the best known approximation ratio is 1.375 [3].
Recently, Dias and Dias [2] presented an extension of the 1.5-approximation algorithm presented by Bafna and Pevzner [1]. The extended version achieves good results in practice, but keeps the original 1.5 approximation ratio. One of the extensions is based on a look-ahead strategy and the impact on time complexity and solution quality was controversial. We conclude in this paper that look-ahead does not worth the increase in time complexity.
Our main contribution is an 1.375-approximation algorithm based on Elias and Hartman [3] approach and on the extended version of Dias and Dias [2]. We intend to provide a method comparable with Dias and Dias regarding solution quality in practical experiments, but improving their approximation ratio.

References

[1]
V. Bafna and P. A. Pevzner. Sorting by Transpositions. SIAM Journal on Discrete Mathematics, 11(2):224--240, May 1998.
[2]
U. Dias and Z. Dias. Extending Bafna-Pevzner Algorithm. In ISB '10: Proceedings of the International Symposium on Biocomputing, pages 1--8. ACM, 2010.
[3]
I. Elias and T. Hartman. A 1.375-Approximation Algorithm for Sorting by Transpositions. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 3(4):369--379, 2006.
[4]
V. J. Fortuna. Distâncias de transposição entre genomas. Master's thesis, Institute of Computing, University of Campinas, 2005.
[5]
A. Labarre. New Bounds and Tractable Instances for the Transposition Distance. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 3(4):380--394, 2006.

Cited By

View all
  • (2022)A new 1.375-approximation algorithm for sorting by transpositionsAlgorithms for Molecular Biology10.1186/s13015-022-00205-z17:1Online publication date: 15-Jan-2022
  • (2022)A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running TimeAdvances in Bioinformatics and Computational Biology10.1007/978-3-031-21175-1_16(147-157)Online publication date: 16-Dec-2022
  • (2015)An Audit Tool for Genome Rearrangement AlgorithmsACM Journal of Experimental Algorithmics10.1145/266163319(1.1-1.34)Online publication date: 7-Jan-2015
  • Show More Cited By

Index Terms

  1. An improved 1.375-approximation algorithm for the transposition distance problem

      Recommendations

      Comments

      Information & Contributors

      Information

      Published In

      cover image ACM Conferences
      BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
      August 2010
      705 pages
      ISBN:9781450304382
      DOI:10.1145/1854776
      Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

      Sponsors

      Publisher

      Association for Computing Machinery

      New York, NY, United States

      Publication History

      Published: 02 August 2010

      Permissions

      Request permissions for this article.

      Check for updates

      Author Tags

      1. genome rearrangement
      2. sorting by transposition

      Qualifiers

      • Research-article

      Funding Sources

      Conference

      BCB'10
      Sponsor:

      Acceptance Rates

      Overall Acceptance Rate 254 of 885 submissions, 29%

      Contributors

      Other Metrics

      Bibliometrics & Citations

      Bibliometrics

      Article Metrics

      • Downloads (Last 12 months)0
      • Downloads (Last 6 weeks)0
      Reflects downloads up to 17 Jan 2025

      Other Metrics

      Citations

      Cited By

      View all
      • (2022)A new 1.375-approximation algorithm for sorting by transpositionsAlgorithms for Molecular Biology10.1186/s13015-022-00205-z17:1Online publication date: 15-Jan-2022
      • (2022)A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running TimeAdvances in Bioinformatics and Computational Biology10.1007/978-3-031-21175-1_16(147-157)Online publication date: 16-Dec-2022
      • (2015)An Audit Tool for Genome Rearrangement AlgorithmsACM Journal of Experimental Algorithmics10.1145/266163319(1.1-1.34)Online publication date: 7-Jan-2015
      • (2013)On the 1.375-Approximation Algorithm for Sorting by Transpositions in O(n logn) Time8th Brazilian Symposium on Advances in Bioinformatics and Computational Biology - Volume 821310.1007/978-3-319-02624-4_12(126-135)Online publication date: 3-Nov-2013
      • (2011)Analysis and Implementation of Sorting by Transpositions Using Permutation TreesAdvances in Bioinformatics and Computational Biology10.1007/978-3-642-22825-4_6(42-49)Online publication date: 2011

      View Options

      Login options

      View options

      PDF

      View or Download as a PDF file.

      PDF

      eReader

      View online with eReader.

      eReader

      Media

      Figures

      Other

      Tables

      Share

      Share

      Share this Publication link

      Share on social media