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Length and Symmetry on the Sorting by Weighted Inversions Problem

Christian Baudet 1 Ulisses Dias 2 Zanoni Dias 2 
1 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Large-scale mutational events that occur when stretches of DNA sequence move throughout genomes are called genome rearrange-ment events. In bacteria, inversions are one of the most frequently ob-served rearrangements. In some bacterial families, inversions are biased in favor of symmetry as shown by recent research [6, 8, 10]. In addition, several results suggest that short segment inversions are more frequent in the evolution of microbial genomes [4,6,15]. Despite the fact that symme-try and length of the reversed segments seem very important, they have not been considered together in any problem in the genome rearrange-ment field. Here, we define the problem of sorting genomes (or permu-tations) using inversions whose costs are assigned based on their lengths and asymmetries. We present five procedures and we assess these proce-dure performances on small sized permutations. The ideas presented in this paper provide insights to solve the problem and set the stage for a proper theoretical analysis.
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Submitted on : Tuesday, December 9, 2014 - 10:09:51 AM
Last modification on : Tuesday, October 25, 2022 - 4:23:50 PM
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Christian Baudet, Ulisses Dias, Zanoni Dias. Length and Symmetry on the Sorting by Weighted Inversions Problem. 9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Horizonte, Brazil. pp.99 - 106, ⟨10.1007/978-3-319-12418-6_13⟩. ⟨hal-01092607⟩



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