Linearizing Genomes: Exact Methods and Local Search

Abstract

International audienceIn this article, we address the problem of genome linearization from the perspective of Polynomial Local Search, a complexity class related to finding local optima. We prove that the linearization problem, with a neighborhood structure, the neighbor slide, is PLS-complete. On the positive side, we develop two exacts methods, one using tree decompositions with an efficient dynamic programming, the other one using an integer linear program. Finally, we compare them on real instances