In 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 exact methods, one using tree decompositions with an efficient dynamic programming, the other using an integer linear programming. Finally, we compare them on real instances.
CITATION STYLE
Davot, T., Chateau, A., Giroudeau, R., & Weller, M. (2020). Linearizing Genomes: Exact Methods and Local Search. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 12011 LNCS, pp. 505–518). Springer. https://doi.org/10.1007/978-3-030-38919-2_41
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