Theory of linear and integer programming
Theory of linear and integer programming
A fast pseudo-boolean constraint solver
Proceedings of the 40th annual Design Automation Conference
Assignment of Orthologous Genes via Genome Rearrangement
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genes order and phylogenetic reconstruction: application to γ-proteobacteria
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Power boosts for cluster tests
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Genomes containing duplicates are hard to compare
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
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Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. Recent researches have resulted in different genomic distance definitions: number of breakpoints, number of common intervals, number of conserved intervals, Maximum Adjacency Disruption number (MAD), etc. Unfortunately, it turns out that, in presence of duplications, most problems are NP-hard, and hence several heuristics have been recently proposed. However, while it is relatively easy to compare heuristics between them, until now very little is known about the absolute accuracy of these heuristics. Therefore, there is a great need for algorithmic approaches that compute exact solutions for these genomic distances. In this paper, we present a novel generic pseudo-boolean approach for computing the exact genomic distance between two whole genomes in presence of duplications, and put strong emphasis on common intervals under the maximum matching model. Of particular importance, we show very strong evidence that the simple LCS heuristic provides very good results on a well-known public benchmark dataset of γ-Proteobacteria.