The Community for Technology Leaders
RSS Icon
Issue No.01 - January-March (2008 vol.5)
pp: 56-66
Genome rearrangement is an important area in computational biology and bioinformatics. The translocation operation is one of the popular operations for genome rearrangement. It was proved that computing the unsigned translocation distance is NP-hard. In this paper, we present a (1.5 + ε)- approximation algorithm for computing unsigned translocation distance which improves upon the best known 1.75-ratio. The running time of our algorithm is O(n^2 + ( 4/ε )^1.5 √log( 4/ε )2 4^ε), where n is the total number of genes in the genome.
Genome rearrangement, unsigned translocation, and approximation algorithms.
Yun Cui, Lusheng Wang, Daming Zhu, Xiaowen Liu, "A (1.5 + ε)-Approximation Algorithm for Unsigned Translocation Distance", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, no. 1, pp. 56-66, January-March 2008, doi:10.1109/TCBB.2007.70216
[1] A. Bergeron, J. Mixtacki, and J. Stoye, “On Sorting by Translocation,” J. Computational Biology, vol. 13, no. 2, pp. 567-578, 2006.
[2] A. Bergeron, S. Heber, and J. Stoye, “Common Intervals and Sorting by Reversals: A Marriage of Necessity,” Bioinformatics, vol. 18, no. Suppl. 2, pp. S54-S63, 2002.
[3] A. Bergeron, “A Very Elementary Presentation of the Hannenhalli-Pevzner Theory,” Discrete Applied Math., vol. 146, no. 2, pp. 134-145, 2005.
[4] Y. Cui, L. Wang, and D. Zhu, “A 1.75-Approximation Algorithm for Unsigned Translocation Distance,” Proc. 16th Int'l Symp. Algorithms and Computation (ISAAC '05), X. Deng and D.-Z. Du, eds., pp. 392-401, 2005. Full version is accepted for publication in J.Computer and System Sciences.
[5] S. Hannenhalli, “Polynomial-Time Algorithm for Computing Translocation Distance between Genomes,” Proc. Sixth Ann. Symp. Combinatorial Pattern Matching (CPM '95), Z. Galil and E.Ukkonen,eds., pp. 162-176, 1995.
[6] S. Hannenhalli and P. Pevzner, “Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals,” Proc. 27th Ann. ACM Symp. Theory of Computing (STOC '95), pp. 178-189, 1995.
[7] J. Kececioglu and R. Ravi, “Of Mice and Men: Algorithms for Evolutionary Distances between Genomes with Translocation,” Proc. Sixth Ann. ACM-SIAM Symp. Discrete Algorithms (SODA '95)), K. Clarkson, ed., pp. 604-613, 1995.
[8] L. Lovász and M.D. Plummer, “Matching Theory,” Annals of Discrete Math., vol. 29, 1986.
[9] M. Ozery-Flato and R. Shamir, “An $O(n^{3/2}\sqrt{\log(n)})$ Algorithm for Sorting by Reciprocal Translocations,” Proc. 17th Ann. Symp. Combinatorial Pattern Matching (CPM '06), M. Lewenstein and G.Valiente, eds., pp.258-269, 2006.
[10] L. Wang, D. Zhu, X. Liu, and S. Ma, “An $O(n^{2})$ Algorithm for Signed Translocation,” J. Computer and System Sciences, vol. 70, pp.284-299, 2005.
[11] D. Zhu and L. Wang, “On the Complexity of Unsigned Translocation Distance,” Theoretical Computer Science, vol. 352, no. 1, pp. 322-328, 2006.
379 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool