Abstract
Comparing genomes of different species has become a crucial problem in comparative genomics. Recent research have resulted in different genomic distance definitions: number of breakpoints, number of common intervals, number of conserved intervals, Maximum Adjacency Disruption number (MAD), etc. Classical methods (usually based on permutations of gene order) for computing genomic distances between whole genomes are however seriously compromised for genomes where several copies of the same gene may be scattered across the genome. Most approaches to overcoming this difficulty are based on the exemplar method (keep exactly one copy in each genome of each duplicated gene) and the maximum matching method (keep as many copies as possible in each genome of each duplicated gene). Unfortunately, it turns out that, in presence of duplications, most problems are NP-hard, and hence several heuristics have been recently proposed.
Extending research initiated in [2], we propose in this paper a novel generic pseudo-boolean approach for computing the exact breakpoint distance between two genomes in presence of duplications for both the exemplar and maximum matching methods. We illustrate the application of this methodology on a well-known public benchmark dataset of γ-Proteobacteria.
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
Angibaud, S., Fertin, G., Rusu, I., Vialette, S.: How pseudo-boolean programming can help genome rearrangement distance computation. In: Bourque, G., El-Mabrouk, N. (eds.) Comparative Genomics. LNCS (LNBI), vol. 4205, pp. 75–86. Springer, Heidelberg (2006)
Angibaud, S., Fertin, G., Rusu, I., Vialette, S.: A general framework for computing rearrangement distances between genomes with duplicates. Journal of Computational Biology 14(4), 379–393 (2007)
Barth, P.: A Davis-Putnam based enumeration algorithm for linear pseudo-boolean optimization. Technical Report MPI-I-95-2-003, Max Planck Institut Informatik, p.13 (2005)
Blin, G., Chauve, C., Fertin, G.: The breakpoint distance for signed sequences. In: Proc. 1st Algorithms and Computational Methods for Biochemical and Evolutionary Networks (Comp. Bio. Nets.), pp. 3–16. KCL publications (2004)
Blin, G., Chauve, C., Fertin, G.: Genes order and phylogenetic reconstruction: Application to γ-proteobacteria. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 11–20. Springer, Heidelberg (2005)
Blin, G., Rizzi, R.: Conserved intervals distance computation between non-trivial genomes. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 22–31. Springer, Heidelberg (2005)
Bourque, G., Yacef, Y., El-Mabrouk, N.: Maximizing synteny blocks to identify ancestral homologs. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 21–35. Springer, Heidelberg (2005)
Bryant, D.: The complexity of calculating exemplar distances. In: Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pp. 207–212. Kluwer Academic Publishers, Dordrecht (2000)
Chai, D., Kuehlmann, A.: A fast pseudo-boolean constraint solver. In: Proc. 40th ACM IEEE Conference on Design Automation, pp. 830–835. ACM Press, New York (2003)
Chauve, C., Fertin, G., Rizzi, R., Vialette, S.: Genomes containing duplicates are hard to compare. In: Alexandrov, V.N., van Albada, G.D., Sloot, P.M.A., Dongarra, J.J. (eds.) ICCS 2006. LNCS, vol. 3992, pp. 783–790. Springer, Heidelberg (2006)
Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Assignment of orthologous genes via genome rearrangement. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(4), 302–315 (2005)
Eén, N., Sörensson, N.: Translating pseudo-boolean constraints into SAT. Journal on Satisfiability, Boolean Modeling and Computation 2, 1–26 (2006)
Lerat, E., Daubin, V., Moran, N.A.: From gene tree to organismal phylogeny in prokaryotes: the case of γ-proteobacteria. PLoS Biology 1(1), 101–109 (2003)
Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic distances under deletions and insertions. Theoretical Computer Science 325(3), 347–360 (2004)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Sankoff, D., Haque, L.: Power boosts for cluster tests. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 11–20. Springer, Heidelberg (2005)
Schrijver, A.: Theory of Linear and Integer Programming. John Wiley and Sons, Chichester (1998)
Sheini, H.M., Sakallah, K.A.: Pueblo: A hybrid pseudo-boolean SAT solver. Journal on Satisfiability, Boolean Modeling and Computation 2, 165–189 (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Angibaud, S., Fertin, G., Rusu, I., Thévenin, A., Vialette, S. (2007). A Pseudo-boolean Programming Approach for Computing the Breakpoint Distance Between Two Genomes with Duplicate Genes . In: Tesler, G., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2007. Lecture Notes in Computer Science(), vol 4751. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74960-8_2
Download citation
DOI: https://doi.org/10.1007/978-3-540-74960-8_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-74959-2
Online ISBN: 978-3-540-74960-8
eBook Packages: Computer ScienceComputer Science (R0)