Genome rearrangements with indels in intergenes restrict the scenario space

Laurent Bulteau 1 Guillaume Fertin 2 Eric Tannier 3, 4
3 BEAGLE - Artificial Evolution and Computational Biology
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
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.
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Laurent Bulteau, Guillaume Fertin, Eric Tannier. Genome rearrangements with indels in intergenes restrict the scenario space. BMC Bioinformatics, BioMed Central, 2016, 17 (Suppl 14), 426 (7 p.). ⟨10.1186/s12859-016-1264-6⟩. ⟨hal-01396842⟩

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