Tandem Halving Problems by DCJ

  • Antoine Thomas
  • Aïda Ouangraoua
  • Jean-Stéphane Varré
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)

Abstract

We address the problem of reconstructing a non-duplicated ancestor to a partially duplicated genome in a model where duplicated content is caused by several tandem duplications throughout its evolution and the only allowed rearrangement operations are DCJ. As a starting point, we consider a variant of the Genome Halving Problem, aiming at reconstructing a tandem duplicated genome instead of the traditional perfectly duplicated genome. We provide a distance in \(\mathcal{O}(n)\) time and a scenario in \(\mathcal{O}(n^2)\) time. In an attempt to enhance our model, we consider several problems related to multiple tandem reconstruction. Unfortunately we show that although the problem of reconstructing a single tandem can be solved polynomially, it is already NP-hard for 2 tandems.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Antoine Thomas
    • 1
  • Aïda Ouangraoua
    • 1
  • Jean-Stéphane Varré
    • 1
  1. 1.LIFL, UMR 8022 CNRSUniversité Lille 1, INRIA LilleVilleneuve d’AscqFrance

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