Abstract
This paper discusses a bit-vector implementation of an algorithm that computes an optimal sequence of reversals that sorts a signed permutation. The main characteristics of the implementation are its simplicity, both in terms of data structures and operations, and the fact that it exploits the parallelism of bitwise logical operations.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
David Bader, Bernard Moret, Mi Yan, A Linear-Time Algorithm for Computing Inversion Distance Between Signed Permutations with an Experiemntal Study. Proc. 7th Workshop on Algs. and Data Structs. WADS01, Providence (2001), to appear in Lecture Notes in Computer Science, Springer Verlag.
Anne Bergeron, A Very Elementary Presentation of the Hannenhalli-Pevzner Theory. CPM 2001, Jerusalem (2001), to appear in Lecture Notes in Computer Science, Springer Verlag.
Piotr Berman and Sridhar Hannenhalli, Fast Sorting by Reversal. CPM 1996, LNCS 1075: 168–185 (1996).
Alberto Caprara, Sorting by reversals is difficult. RECOMB 1997, ACM Press: 75–83 (1997).
Sridhar Hannenhalli and Pavel Pevzner, Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals. JACM 46(1): 1–27 (1999).
John Kececioglu and David Sankoff, Efficient bounds for oriented chromosome-inversion distance. CPM 1994, LNCS 807: 307–325 (1994).
Haim Kaplan, Ron Shamir, Robert Tarjan, A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. SIAM J. Comput. 29(3): 880–892 (1999).
Pavel Pevzner, Computational Molecular Biology, MIT Press, Cambridge, Mass., 314 pp. (2000).
David Sankoff, Edit Distances for Genome Comparisons Based on Non-Local Operations. CPM 1992, LNCS 644: 121–135 (1992).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2001 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bergeron, A., Strasbourg, F. (2001). Experiments in Computing Sequences of Reversals. In: Gascuel, O., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2001. Lecture Notes in Computer Science, vol 2149. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44696-6_13
Download citation
DOI: https://doi.org/10.1007/3-540-44696-6_13
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-42516-8
Online ISBN: 978-3-540-44696-5
eBook Packages: Springer Book Archive