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
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
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
How pseudo-boolean programming can help genome rearrangement distance computation
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Genomes containing duplicates are hard to compare
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
The ExemplarBreakpointDistance for Non-trivial Genomes Cannot Be Approximated
WALCOM '09 Proceedings of the 3rd International Workshop on Algorithms and Computation
A polynomial algebra method for computing exemplar breakpoint distance
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
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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.