Abstract
The study of genome rearrangements is an important tool in comparative genomics. This paper revisits the problem of sorting a multichromosomal genome by translocations, i.e. exchanges of chromosome ends. We give an elementary proof of the formula for computing the translocation distance in linear time, and we give a new algorithm for sorting by translocations, correcting an error in a previous algorithm by Hannenhalli.
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
Bergeron, A., Mixtacki, J., Stoye, J.: Reversal distance without hurdles and fortresses. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 388–399. Springer, Heidelberg (2004)
Bergeron, A., Mixtacki, J., Stoye, J.: The inversion distance problem. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny, ch. 10, pp. 262–290. Oxford University Press, Oxford (2005)
Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)
Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
Hannenhalli, S.: Polynomial-time algorithm for computing translocation distance between genomes. Discrete Appl. Math. 71(1-3), 137–151 (1996)
Hannenhalli, S., Pevzner, P.A.: Transforming men into mice, polynomial algorithm for genomic distance problem. In: FOCS 1995 Proceedings, pp. 581–592. IEEE Press, Los Alamitos (1995)
Kececioglu, J.D., Ravi, R.: Of mice and men: Algorithms for evolutionary distances between genomes with translocation. In: Proceedings of the sixth ACM-SIAM Symposium on Discrete Algorithm. pp. 604–613. Society of Industrial and Applied Mathematics (1995)
Li, G., Qi, X., Wang, X., Zhu, B.: A linear-time algorithm for computing translocation distance between signed genomes. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 323–332. Springer, Heidelberg (2004)
Ozery-Flato, M., Shamir, R.: Two notes on genome rearrangements. J. Bioinf. Comput. Biol. 1(1), 71–94 (2003)
Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. J. Comput. Syst. Sci. 65(3), 587–609 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bergeron, A., Mixtacki, J., Stoye, J. (2005). On Sorting by Translocations. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_47
Download citation
DOI: https://doi.org/10.1007/11415770_47
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25866-7
Online ISBN: 978-3-540-31950-4
eBook Packages: Computer ScienceComputer Science (R0)