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ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin 1 Jean-Stéphane Varré 1 Samuel Blanquart 1 Aïda Ouangraoua 1
1 BONSAI - Bioinformatics and Sequence Analysis
Université de Lille, Sciences et Technologies, Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189, CNRS - Centre National de la Recherche Scientifique
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.CONCLUSION: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, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/ webcite.
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Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics, BioMed Central, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩. ⟨hal-01217311⟩

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