Abstract
During evolution, chromosomal rearrangements, such as reciprocal translocation, transposition and inversion, disrupt gene content and gene order on chromosomes. We discuss algorithmic and statistical approaches to the analysis of comparative genomic data. In a phylogenetic context, a combined approach is suggested, leading to the median problem for breakpoints. We solve this problem first for the case where all genomes have the same gene content, and then for the general case.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
References
V. Bafna and P.A. Pevzner. Genome rearrangements and sorting by reversals. SIAM Journal of Computing 25:272–289, 1996.
V. Bafna and P.A. Pevzner. Sorting by transpositions. Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 614–623, 1995.
M. Blanchette, T. Kunisawa and D. Sankoff. Parametric genome rearrangement. Gene 172, GC 11–17, 1996.
A. Caprara. Sorting by Reversals is Difficult. Proceeedings of the First Annual International Conference on Computational Molecular Biology (RECOMB 97), 75–83, 1997.
B. DasGupta, T.Jiang, S.Kannan, M.Li, Z. Sweedyk. On the Complexity and Approximation of Syntenic Distance. Proceeedings of the First Annual International Conference on Computational Molecular Biology (RECOMB 97), 99–108, 1997.
V. Ferretti, J.H. Nadeau and D. Sankoff. Original synteny. Proceedings of the Seventh Annual Symposium on Combinatorial Pattern Matching, D. Hirschberg and G. Myers ed., Springer Verlag Lecture Notes in Computer Science, 1075: 159–167, 1996.
S. Hannenhalli. Polynomial algorithm for computing translocation distance between genomes. Proceedings of the 6th Symposium on Combinatorial Pattern Matching, Springer Verlag Lecture Notes in Computer Science: 162–176, 1995.
S. Hannenhalli and P.A. Pevzner, Transforming cabbage into turnip. (polynomial algorithm for sorting signed permutations by reversals). Proceedings of the 27th Annual ACM-SIAM Symposium on the Theory of Computing, pp. 178–189, 1995.
S. Hannenhalli and P.A. Pevzner. Transforming men into mice (polynomial algorithm for genomic distance problem). Proceedings of the IEEE 36th Annual Symposium on Foundations of Computer Science, 581–592, 1995.
H. Kaplan, R. Shamir, and R.E. Tarjan. Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. Proceeedings of the Eighth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 97), 1997.
J. Kececioglu and R. Ravi. Of mice and men. Evolutionary distances between genomes under translocation. Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 604–613, 1995.
J. Kececioglu and D. Sankoff. Efficient bounds for oriented chromosome inversion distance. Proceedings of the 5th Symposium on Combinatorial Pattern Matching, Springer Verlag Lecture Notes in Computer Science 807:307–325. 1994.
J. Kececioglu and D. Sankoff. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica, 13:180–210, 1995.
I. Marchand. Généralisations du modèle de Nadeau et Taylor sur les segments chromosomiques conservés, MSc thesis, Département de mathématiques et de statistique, Université de Montréal. 1997.
E. Minieka, Optimization Algorithms for Networks and Graphs, Industrial Engineering vol. 1, New York: Marcel Dekker, chap. 7.3. pp. 272–273, 1978
J.H. Nadeau and B.A. Taylor Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences USA, 81: 814–818, 1984.
M.-N. Parent. Estimation du nombre de segments vides dans le modèle de Nadeau et Taylor sur les segments chromosomiques conservés. MSc thesis, Département de mathématiques et de statistique, Université de Montréal. 1997.
D. Sankoff. Edit distance for genome comparison based on non-local operations. Proceedings of the 3rd Symposium on Combinatorial Pattern Matching, Verlag Lecture Notes in Computer Science 644:121–135. 1992.
D. Sankoff and V. Ferretti. Karotype distributions in a stochastic model of reciprocal translocation. Genome Research 6, 1–9, 1996.
D. Sankoff, V. Ferretti and J.H. Nadeau. Conserved segment identification. RECOMB 97. Proceedings of the First Annual International Conference on Computational Molecular Biology. New York: ACM Press, 1997, pp. 252–256. revised version to appear in Journal of Computational Biology..
D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B.F. Lang, and R. Cedergren. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences USA 89, 6575–6579, 1992.
D. Sankoff, G. Sundaram and J. Kececioglu. Steiner points in the space of genome rearrangements. International Journal of the Foundations of Computer Science 7, 1–9,1996
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1997 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Sankoff, D., Blanchette, M. (1997). The median problem for breakpoints in comparative genomics. In: Jiang, T., Lee, D.T. (eds) Computing and Combinatorics. COCOON 1997. Lecture Notes in Computer Science, vol 1276. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0045092
Download citation
DOI: https://doi.org/10.1007/BFb0045092
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-63357-0
Online ISBN: 978-3-540-69522-6
eBook Packages: Springer Book Archive