Abstract
The study of evolution based on rearrangements leads to a rearrangement distance problem, i.e., computing the minimum number of rearrangement events required to transform one geonome to another. In this paper we study the translocation distance problem, modeling the evolution of genomes by translocations. We present a linear-time algorithm for computing the translocation distance between signed genomes in this paper, improving a previous O(n 3) bound by Hannenhalli in 1996.
This research is partially supported by NSFC under Grants 10271065 and 60373025.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Sankoff, D.: Edit distance for genomes comparison based on non-local operation. In: Apostolico, A., Galil, Z., Manber, U., Crochemore, M. (eds.) CPM 1992. LNCS, vol. 644, pp. 121–135. Springer, Heidelberg (1992)
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B., Cedergren, R.: Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. In: Proc. Nat. Sci. USA, vol. 89, pp. 6575–6579 (1992)
Hannenhalli, S.: Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied Mathematics 71, 137–151 (1996)
Bader, D., Moret, B., Yan, M.: A linear-time algorithm for computing inversion distance between signed permutations with experimental study. J. Comput. Biol. 8, 483–491 (2001)
Bafna, V., Pevzner, P.: Genome rearrangements and sorting by reversals. SIAM J. Comput. 25, 272–289 (1996)
Kececioglu, J., Sankoff, D.: Exact and approximation algorithms for the reversal distance between two permutation. J. Algorithms 13(1/2), 180–210 (1995)
Hannenhalli, S., Pevzner, P.: Transforming men into mice-polynomial algorithm for computing genomic distance problem. In: Proc. 36th IEEE Symposium on Foundations of Computer Science, pp. 581–592 (1995)
Kececioglu, J., Ravi, R.: Of mice and men: evolutionary distances between genomes under translocation. In: Proc. 6th Ann. ACM-SIAM Symp. on Discrete Algorithms, pp. 604–613 (1995)
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
Li, G., Qi, X., Wang, X., Zhu, B. (2004). A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes. In: Sahinalp, S.C., Muthukrishnan, S., Dogrusoz, U. (eds) Combinatorial Pattern Matching. CPM 2004. Lecture Notes in Computer Science, vol 3109. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27801-6_24
Download citation
DOI: https://doi.org/10.1007/978-3-540-27801-6_24
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22341-2
Online ISBN: 978-3-540-27801-6
eBook Packages: Springer Book Archive