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Linearizing Genomes: Exact Methods and Local Search

  • Tom DavotEmail author
  • Annie Chateau
  • Rodolphe Giroudeau
  • Mathias Weller
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 12011)

Abstract

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.

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Tom Davot
    • 1
    Email author
  • Annie Chateau
    • 1
  • Rodolphe Giroudeau
    • 1
  • Mathias Weller
    • 2
  1. 1.LIRMM - CNRS UMR 5506MontpellierFrance
  2. 2.CNRS, LIGM (UMR 8049)Champs-s/-MarneFrance

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