ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin 1 Jean-Stéphane Varré 2, 1 Samuel Blanquart 1 Aïda Ouangraoua 1, *
* Auteur correspondant
1 BONSAI - Bioinformatics and Sequence Analysis
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : Background: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program is written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/.
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Communication dans un congrès
ISCB-Latin America, Oct 2014, Belo Horizonte, Brazil. 2014, 〈http://www.iscb.org/iscb-latinamerica2014〉
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Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. ISCB-Latin America, Oct 2014, Belo Horizonte, Brazil. 2014, 〈http://www.iscb.org/iscb-latinamerica2014〉. 〈hal-01083841〉

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