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Tandem Halving Problems by DCJ

Antoine Thomas 1 Aïda Ouangraoua 1, * Jean-Stéphane Varré 1, 2, *
* Corresponding author
1 BONSAI - Bioinformatics and Sequence Analysis
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
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 O(n) time and a scenario in O(n2) 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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Submitted on : Tuesday, November 6, 2012 - 2:48:53 PM
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Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré. Tandem Halving Problems by DCJ. Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.417-429, ⟨10.1007/978-3-642-33122-0_33⟩. ⟨hal-00749019⟩

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