title: A pseudo-boolean framework for computing rearrangement distances between genomes with duplicates.
abstract: Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. Recent researches have resulted in different genomic distance definitions, for example, number of breakpoints, number of common intervals, number of conserved intervals, and Maximum Adjacency Disruption number. 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 three heuristics which provide very good results on a well-known public dataset of gamma-Proteobacteria.
authors.affiliation: Laboratoire d'Informatique de Nantes-Atlantique, FRE CNRS 2729, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France. Sebastien.Angibaud@univ-nantes.fr
authors.forename: Sébastien
authors.initials: S
authors.lastname: Angibaud
authors.forename: Guillaume
authors.initials: G
authors.lastname: Fertin
authors.forename: Irena
authors.initials: I
authors.lastname: Rusu
authors.forename: Stéphane
authors.initials: S
authors.lastname: Vialette
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D020563:Gammaproteobacteria / Q000235:genetics*; D020440:Gene Duplication; D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA; D012984:Software