Busca avançada
Ano de início
Entree
(Referência obtida automaticamente do Web of Science, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores.)

Sorting by weighted inversions considering length and symmetry

Texto completo
Autor(es):
Baudet, Christian [1] ; Dias, Ulisses [2] ; Dias, Zanoni [3]
Número total de Autores: 3
Afiliação do(s) autor(es):
[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
Número total de Afiliações: 3
Tipo de documento: Artigo Científico
Fonte: BMC Bioinformatics; v. 16, n. 19 DEC 16 2015.
Citações Web of Science: 3
Resumo

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)

Processo FAPESP: 14/19401-8 - Algoritmos para rearranjos de genomas
Beneficiário:Zanoni Dias
Linha de fomento: Auxílio à Pesquisa - Regular
Processo FAPESP: 12/01584-3 - Problemas de distâncias de rearranjos de genomas
Beneficiário:Ulisses Martins Dias
Linha de fomento: Bolsas no Brasil - Pós-Doutorado
Processo FAPESP: 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais
Beneficiário:Munir Salomao Skaf
Linha de fomento: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs