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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Sorting by weighted inversions considering length and symmetry

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Baudet, Christian [1] ; Dias, Ulisses [2] ; Dias, Zanoni [3]
Total Authors: 3
[1] Univ Lyon 1, Inria Erable Team, F-69622 Villeurbanne - France
[2] Univ Estadual Campinas, Fac Technol, BR-13484332 Limeira - Brazil
[3] Univ Estadual Campinas, Inst Comp, BR-13083852 Campinas, SP - Brazil
Total Affiliations: 3
Document type: Journal article
Source: BMC Bioinformatics; v. 16, n. 19 DEC 16 2015.
Web of Science Citations: 3

Large-scale mutational events that occur when stretches of DNA sequence move throughout genomes are called genome rearrangements. In bacteria, inversions are one of the most frequently observed rearrangements. In some bacterial families, inversions are biased in favor of symmetry as shown by recent research. In addition, several results suggest that short segment inversions are more frequent in the evolution of microbial genomes. Despite the fact that symmetry and length of the reversed segments seem very important, they have not been considered together in any problem in the genome rearrangement field. Here, we define the problem of sorting genomes (or permutations) using inversions whose costs are assigned based on their lengths and asymmetries. We consider two formulations of the same problem depending on whether we know the orientation of the genes. Several procedures are presented and we assess these procedure performances on a large set of more than 4.4 x 10(9) permutations. The ideas presented in this paper provide insights to solve the problem and set the stage for a proper theoretical analysis. (AU)

FAPESP's process: 14/19401-8 - Genome rearrangement algorithms
Grantee:Zanoni Dias
Support type: Regular Research Grants
FAPESP's process: 12/01584-3 - Genome Rearrangement Distance Problems
Grantee:Ulisses Martins Dias
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC