Asimpler and faster 1.5-approximation algorithm for sorting by transpositions

Information and Computation

Volumn 204, Issue 2, 2006, Pages 275-290

  Hartman, Tzvika ^a   Shamir, Ron ^b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Computational biology; Genome rearrangements; Sorting permutations by transpositions

Indexed keywords

GENES;

CHRISTIE; CIRCULAR PERMUTATION; COMPUTATIONAL BIOLOGY; GENOME REARRANGEMENTS; LINEAR PERMUTATION; QUADRATIC ALGORITHMS; SORTING BY TRANSPOSITIONS; SORTING PERMUTATIONS BY TRANSPOSITIONS;

APPROXIMATION ALGORITHMS;

EID: 84855205127     PISSN: 08905401     EISSN: 10902651     Source Type: Journal    
DOI: 10.1016/j.ic.2005.09.002     Document Type: Article

References (31)

1. D. A. Bader, B. M. E. Moret, M. Yan, A linear-time algorithm for computing inversion distance between signed permutations with an experimental study, J. Comput. Biol. 8(5) (2001) 483-491. (Pubitemid 33044073)
2. V. Bafna, P. A. Pevzner, Genome rearragements and sorting by reversals, SIAM J. Comput. 25(2) (1996) 272-289.
3. V. Bafna, P. A. Pevzner, Sorting by transpositions, SIAM J. Discrete Math. 11(2) (1998) 224-240. (Pubitemid 128619806)
4. A. Bergeron. A very elementary presentation of the Hannenhalli-Pevzner theory, in: Proceedings of 12th Annual Symposium on Combinatorial Pattern Matching (CPM'01), 2001.
5. P. Berman, S. Hannanhalli, M. Karpinski, 1.375-approximation algorithm for sorting by reversals, in: Proceedings of 10th European Symposium on Algorithms (ESA'02), Lecture Notes in Computer Science, vol. 2461, Springer, 2002, pp. 200-210.
6. A. Caprara, Sorting permutations by reversals and Eulerian cycle decompositions, SIAM J. Discrete Math. 12(1) (1999) 91-110.
7. D. A. Christie, A3/2-approximation algorithm for sorting by reversals, in: Proceedings of Ninth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 98), ACM Press, 1998, pp. 244-252.
8. D. A. Christie, Genome Rearrangement Problems. PhD thesis, University of Glasgow, 1999.
9. I. Elias, T. Hartman, A1.375-approximation algorithm for sorting bytranspositions, in: Proceedingsof 5th Workshop on Algorithms in Bioinformatics (WABI'05), LNBI 3692, 2005, pp. 204-215.
10. H. Eriksson, K. Eriksson, J. Karlander, L. Svensson, J. Wastlund, Sorting a bridge hand, Discrete Math. 241 (1-3) (2001) 289-300. (Pubitemid 33673697)
11. Q. P. Gu, S. Peng, H. Sudborough, A2-approximation algorithm for genome rearrangements by reversals and transpositions, Theor. Comput. Sci. 210(2) (1999) 327-339. (Pubitemid 129611357)
12. S. Hannenhalli, P. Pevzner, Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals, J. ACM 46(1999) 1-27
13. (Preliminary version in Proceedings of the Twenty-Seventh Annual ACM Symposium on Theory of Computing 1995 (STOC 95), pp. 178-189)..
14. T. Hartman, Asimpler 1.5-approximation algorithm for sorting by transpositions, in: Proceedings 14th Annual Symposium on Combinaotrial Pattern Matching (CPM'03), Springer, 2003, pp. 156-169.
15. T. Hartman, R. Sharan, A1.5-approximation algorithm for sorting by transpositions and transreversals, J. Comput. Syst. Sci. 70(2005) 300-320. (Pubitemid 40391412)
16. M. I. Honda, Implementation of the Algorithm of Hartman for the Problem of Sorting by Transpositions, Master Thesis, 2004.
17. S. B. Hoot, J. D. Palmer, Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera, J. Mol. Evol. 38(1994) 274-281. (Pubitemid 24076866)
18. H. Kaplan, R. Shamir, R. E. Tarjan, Faster and simpler algorithm for sorting signed permutations by reversals, SIAM J. Comput. 29(3) (2000) 880-892
19. (Preliminary version in Proceedings of the eighth annual ACM-SIAM Symposium on Discrete Algorithms 1997 (SODA 97), ACM Press, pp. 344-351).
20. H. Kaplan, E. Verbin, Efficient data structures and a new randomized approach for sorting signed permutations by reversals, in: Proceedings 14th Annual Symposium on Combinaotrial Pattern Matching (CPM'03), Springer, 2003, pp. 170-185.
21. G. H. Lin, G. Xue, Signed genome rearrangements by reversals and transpositions: models and approximations, Theor. Comput. Sci. 259(2001) 513-531. (Pubitemid 32674041)
22. J. Meidanis, M. E. Walter, Z. Dias, Reversal distance of signed circular chromosomes, Technical report IC-00-23, Institute of Computing, University of Campinas, December 2000.
23. J. D. Palmer, L. A. Herbon, Tricircular mitochondrial genomes of Brassica and Raphanus: reversal of repeat configurations by inversion, Nucleic Acids Res. 14(1986) 9755-9764.
24. P. A. Pevzner, Computational Molecular Biology: An Algorithmic Approach, MIT Press, Cambridge, MA, 2000.
25. D. Sankoff, N. El-Mabrouk, Genome rearrangement, in: T. Jiang, T. Smith, Y. Xu, M. Q. Zhang (Eds.), Current Topics in Computational Molecular Biology, MIT Press, Cambridge, MA, 2002.
26. J. Setubal, J. Meidanis, Introduction to Computational Biology, PWS Publishing, 1997.
27. R. Shamir, Algorithms in molecular biology: lecture notes. 2002. Available from: .
28. D. D. Sleator, R. E. Tarjan, Self-adjusting binary search trees, J. Assoc. Comput. Mach. 32(1985) 652-686.
29. M. E. Walter, Z. Dias, J. Meidanis, Reversal and transposition distance of linear chromosomes, in: String Processing and Information Retrieval: ASouth American Symposium (SPIRE 98), 1998.
30. M. E. Walter, L. Reginaldo, A. F. Curado, A. G. Oliveira, Working on the problem of sorting by transpositions on genome rearrangements, in: Proceedings of 14th Annual Symposium on Combinatorial Pattern Matching (CPM'03), Springer, 2003, pp. 372-383.
31. M. E. Walter, M. C. Sobrinho, E. T. G. Oliviera, L. S. Soares, A. G. Oliviera, T. E. S. Martins, T. G. Fonseca, Improving the algorithm of Bafna and Pevzver for the problem of sorting by transpositions: a practical approach, in: Proceedings of Second Brazilian Workshop on Bioinformatics (WOB'03), 2003.