Genome rearrangements with indels in intergenes restrict the scenario space

BMC Bioinformatics

Research

Guillaume Fertin¹  Eric Tannier²  Laurent Bulteau³ 

[1] LINA UMR CNRS 6241, Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France;Laboratoire de Biométrie et Biologie Évolutive (LBBE), 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France;Institut National de Recherche en Informatique et en Automatique (INRIA) Rhône-Alpes, 655 avenue de l’Europe, 38330, Montbonnot-Saint-Martin, France;Laboratoire d’Informatique Gaspard Monge, CNRS UMR 8049, Université Paris-Est, 5 Bd Descartes, 77454, Marne-la-Vallée, France;

关键词: DCJ;    Intergenic regions;    Indels;    Genome rearrangements;   

DOI  :  10.1186/s12859-016-1264-6

来源: Springer

【 摘 要 】

BackgroundGiven two genomes that have diverged by a series of rearrangements, we infer minimum Double Cut-and-Join (DCJ) scenarios to explain their organization differences, coupled with indel scenarios to explain their intergene size distribution, where DCJs themselves also alter the sizes of broken intergenes.ResultsWe give a polynomial-time algorithm that, given two genomes with arbitrary intergene size distributions, outputs a DCJ scenario which optimizes on the number of DCJs, and given this optimal number of DCJs, optimizes on the total sum of the sizes of the indels.ConclusionsWe show that there is a valuable information in the intergene sizes concerning the rearrangement scenario itself. On simulated data we show that statistical properties of the inferred scenarios are closer to the true ones than DCJ only scenarios, i.e. scenarios which do not handle intergene sizes.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

Fig. 2