Abstract
The increasing number of fully sequenced genomes has led to the study of genome rearrangements. Several approaches have been proposed to solve this problem, all of them being either too complex to be solved efficiently or too simple to be applied to genomes of complex organisms. The latest challenge has been to overcome the problem of having genomes with duplicate genes. This led to the definition of matching models and similarity measures. The idea is to find a matching between genes in two genomes, in order to disambiguate the data of duplicate genes and calculate a similarity measure. The problem becomes that of finding a matching that best preserves the order of genes in two genomes, where gene order is evaluated by a chosen similarity measure. This paper presents a new pseudo-Boolean encoding for computing the exact summed adjacency disruption number for two genomes with duplicate genes. Experimental results on a γ-Proteobacteria data set illustrate the approach.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Angibaud, S., Fertin, G., Rusu, I., Thévenin, A., Vialette, S.: Efficient tools for computing the number of breakpoints and the number of adjacencies between two genomes with duplicate genes. Journal of Computational Biology 15(8), 1093–1115 (2008)
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)
Bafna, V., Pevzner, P.A.: Sorting by reversals: Genome rearrangements in plant organneles and evolutionary history of x chromosome. Molecular Biology and Evolution 12(2), 239–246 (1995)
Bafna, V., Pevzner, P.A.: Genome rearrangements and sorting by reversals. SIAM Journal on Computing 25(2), 272–289 (1996)
Barth, P.: A Davis-Putnam enumeration algorithm for linear pseudo-Boolean optimization. Technical Report MPI-I-95-2-003, Max Plank Institute for CS (1995)
Blin, G., Chauve, C., Fertin, G.: Genes order and phylogenetic reconstruction: Application to γ-protobacteria. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 11–20. Springer, Heidelberg (2005)
Blin, G., Chauve, C., Fertin, G., Rizzi, R., Vialette, S.: Comparing genomes with duplications: a computational complexity point of view. IEEE/ACM Transactions on Computational Biology and Bioinformatics 4(4), 523–534 (2007)
Caprara, A., Lancia, G., Ng, S.K.: A column-generation based branch-and-bound algorithm for sorting by reversals. In: Mathematical Support for Molecular Biology. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 47, pp. 213–226 (1999)
Delgado, J.: Pseudo-boolean approaches to comparative genomics. Master’s thesis, Instituto Superior Técnico, Technical University of Lisbon, Portugal (June 2009)
Eén, N., Sörensson, N.: Translating pseudo-boolean constraints into sat. Journal on Satisfiability, Boolean Modeling and Computation 2, 1–26 (2006)
Kececioglu, J., Ravi, R.: Of mice and men: Evolutionary distances between genomes under translocations. In: 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 604–613 (1995)
Kececioglu, J., Sankoff, D.: Exact and approximation algorithms for sorting by reversals, with application to genome rearrangements. Algorithmica 13, 180–210 (1995)
Lerat, E., Daubin, V., Moran, N.A.: From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biology 1(1), 101–109 (2003)
Li, W.-H., Gu, Z., Wang, H., Nekrutenko, A.: Evolutionary analyses of the human genome. Nature 409, 847–849 (2001)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Sankoff, D.: Gene and genome duplication. Current Opinion in Genetics & Development 11(6), 681–684 (2001)
Sankoff, D., Haque, L.: Power boost for cluster tests. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 121–130. Springer, Heidelberg (2005)
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., Cedergren, R.: Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences of the United States of America 89(14), 6575–6579 (1992)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Delgado, J., Lynce, I., Manquinho, V. (2009). Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes Using Pseudo-Boolean Optimization. In: Ciccarelli, F.D., Miklós, I. (eds) Comparative Genomics. RECOMB-CG 2009. Lecture Notes in Computer Science(), vol 5817. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04744-2_12
Download citation
DOI: https://doi.org/10.1007/978-3-642-04744-2_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04743-5
Online ISBN: 978-3-642-04744-2
eBook Packages: Computer ScienceComputer Science (R0)