Genome rearrangements with indels in intergenes restrict the scenario space. Issue 14 (November 2016)

• Record Type: Journal Article
• Authors: Bulteau, Laurent; Fertin, Guillaume; Tannier, Eric
• Is Part Of: BMC bioinformatics. Volume 17:Issue 14(2016)
• Page Start: 225
• Page End: 231
• Publication Date: 2016-11
• Subjects: DCJ -- Intergenic regions -- Indels -- Genome rearrangements; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-016-1264-6
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Given 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. Results We 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. Conclusions We 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.