title: An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.
abstract: Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be computed in linear time for genomes without duplicate genes, while the problem becomes NP-hard in the presence of duplicate genes. In this article, we propose an integer linear programming (ILP) formulation to compute the DCJ distance between two genomes with duplicate genes. We also provide an efficient preprocessing approach to simplify the ILP formulation while preserving optimality. Comparison on simulated genomes demonstrates that our method outperforms MSOAR in computing the edit distance, especially when the genomes contain long duplicated segments. We also apply our method to assign orthologous gene pairs among human, mouse, and rat genomes, where once again our method outperforms MSOAR.
authors.affiliation: 1 Laboratory for Computational Biology and Bioinformatics, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, Switzerland .
authors.forename: Mingfu
authors.initials: M
authors.lastname: Shao
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.forename: Bernard M E
authors.initials: BM
authors.lastname: Moret
mesh_terms: D000465:Algorithms; D000818:Animals; D005075:Biological Evolution; D020131:Genes, Duplicate; D016678:Genome; D023281:Genomics / Q000379:methods / Q000706:statistics & numerical data*; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D011382:Programming, Linear; D051381:Rats
keywords: DCJ distance; adjacency graph; maximum cycle decomposition; orthology assignment