Abstract
One of the most promising ways to determine evolutionary distance between two organisms is to compare the order of appearance of orthologous genes in their genomes. The resulting genome rearrangement problem calls for finding a shortest sequence of rearrangement operations that sorts one genome into the other. In this paper we provide a 1.5-approximation algorithm for the problem of sorting by transpositions and transreversals, improving on a five years old 1.75 ratio for this problem. Our algorithm is also faster than current approaches and requires \(O(n^{3/2} \sqrt{\log{n}})\) time for n genes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Palmer, J.D., Herbon, L.A.: Tricircular mitochondrial genomes of Brassica and Raphanus: reversal of repeat configurations by inversion. Nucleic Acids Research 14, 9755–9764 (1986)
Hoot, S.B., Palmer, J.D.: Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. J. Molecular Evooution 38, 274–281 (1994)
Caprara, A.: Sorting permutations by reversals and Eulerian cycle decompositions. SIAM Journal on Discrete Mathematics 12, 91–110 (1999)
Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM 46, 1–27 (1999)
Bafna, V., Pevzner, P.A.: Sorting by transpositions. SIAM Journal on Discrete Mathematics 11, 224–240 (1998)
Christie, D.A.: Genome Rearrangement Problems. PhD thesis, University of Glasgow (1999)
Hartman, T.: A simpler 1.5-approximation algorithm for sorting by transpositions. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 156–169. Springer, Heidelberg (2003)
Gu, Q.P., Peng, S., Sudborough, H.: A 2-approximation algorithm for genome rearrangements by reversals and transpositions. Theoretical Computer Science 210(2), 327–339 (1999)
Lin, G.H., Xue, G.: Signed genome rearrangements by reversals and transpositions: Models and approximations. In: Asano, T., Imai, H., Lee, D.T., Nakano, S.-i., Tokuyama, T. (eds.) COCOON 1999. LNCS, vol. 1627, pp. 71–80. Springer, Heidelberg (1999)
Meidanis, J., Walter, M.E., Dias, Z.: Reversal distance of signed circular chromosomes (2000) (manuscript)
Bafna, V., Pevzner, P.A.: Genome rearragements and sorting by reversals. SIAM Journal on Computing 25, 272–289 (1996)
Kaplan, H., Verbin, E.: Effficient data structures and a new randomized approach for sorting signed permutations by reversals. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 170–185. Springer, Heidelberg (2003)
Sleator, D.D., Tarjan, R.E.: Self-adjusting binary search trees. J. Assoc. Comput. Mach. 32, 652–686 (1985)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hartman, T., Sharan, R. (2004). A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_5
Download citation
DOI: https://doi.org/10.1007/978-3-540-30219-3_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-23018-2
Online ISBN: 978-3-540-30219-3
eBook Packages: Springer Book Archive