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
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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Sérgio Campos. 9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Horizonte, Brazil. Lecture Notes in Computer Science, 8826, pp.99 - 106, 2014, Advances in Bioinformatics and Computational Biology. 〈10.1007/978-3-319-12418-6_13〉
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Christian Baudet, Ulisses Dias, Zanoni Dias. Length and Symmetry on the Sorting by Weighted Inversions Problem. Sérgio Campos. 9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Horizonte, Brazil. Lecture Notes in Computer Science, 8826, pp.99 - 106, 2014, Advances in Bioinformatics and Computational Biology. 〈10.1007/978-3-319-12418-6_13〉. 〈hal-01092607〉

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