Abstract
Sorting by Transpositions is an NP-hard problem for which several polynomial time approximation algorithms have been developed. Hartman and Shamir (2006) developed a 1.5-approximation algorithm, whose running time was improved to O(n logn) by Feng and Zhu (2007) with a data structure they defined, the permutation tree. Elias and Hartman (2006) developed a 1.375-approximation algorithm that runs in O(n 2) time. In this paper, we propose the first correct adaptation of this algorithm to run in O(n logn) time.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
References
Bafna, V., Pevzner, P.A.: Sorting by transpositions. SIAM J. Discrete Math. 11(2), 224–240 (1998)
Bulteau, L., Fertin, G., Rusu, I.: Sorting by transpositions is difficult. SIAM J. Discrete Math. 26(3), 1148–1180 (2012)
Christie, D.A.: Genome Rearrangement Problems. Ph.D. thesis, University of Glasgow, UK (1999)
Cunha, L.F.I., Kowada, L.A.B., de A. Hausen, R., de Figueiredo, C.M.H.: On the 1.375-approximation algorithm for sorting by transpositions in o(n logn) time. In: Setubal, J.C., Almeida, N.F. (eds.) BSB 2013. LNCS, vol. 8213, pp. 126–135. Springer, Heidelberg (2013)
Elias, I., Hartman, T.: A 1.375-approximation algorithm for sorting by transpositions. IEEE/ACM Trans. Comput. Biol. Bioinformatics 3(4), 369–379 (2006)
Feng, J., Zhu, D.: Faster algorithms for sorting by transpositions and sorting by block interchanges. ACM Trans. Algorithms 3(3), 1549–6325 (2007)
Firoz, J.S., Hasan, M., Khan, A.Z., Rahman, M.S.: The 1.375 approximation algorithm for sorting by transpositions can run in \(\uppercase{O}(n \log n)\) time. J. Comput. Biol. 18(8), 1007–1011 (2011)
Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. J. ACM 46(1), 1–27 (1999)
Hartman, T., Shamir, R.: A simpler and faster 1.5-approximation algorithm for sorting by transpositions. Inf. Comput. 204(2), 275–290 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Cunha, L.F.I., Kowada, L.A.B., de A. Hausen, R., de Figueiredo, C.M.H. (2014). A Faster 1.375-Approximation Algorithm for Sorting by Transpositions. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_3
Download citation
DOI: https://doi.org/10.1007/978-3-662-44753-6_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-44752-9
Online ISBN: 978-3-662-44753-6
eBook Packages: Computer ScienceComputer Science (R0)