ProCARs: Progressive Reconstruction of Ancestral Gene Orders. (December 2015)

• Record Type: Journal Article
• Authors: Perrin, Amandine; Varré, Jean-Stéphane; Blanquart, Samuel; Ouangraoua, Aïda
• Is Part Of: BMC genomics. Volume 16:Number 5(2015)
• Page Start: 1
• Page End: 11
• Publication Date: 2015-12
• Subjects: Ancestral gene orders reconstruction -- Small phylogeny problem -- Boreoeutherian ancestor; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/1471-2164-16-S5-S6
• Languages: English
• ISSNs: 1471-2164

Abstract

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 athttp://bioinfo.lifl.fr/procars/ .