Sorting permutations and binary strings by length-weighted rearrangements

Autor(es)

Lintzmayer, Carla Negri ^[1] ; Fertin, Guillaume ^[2] ; Dias, Zanoni ^[1]

Afiliação do(s) autor(es)

^[1] Univ Estadual Campinas, Inst Comp, Campinas, SP - Brazil

^[2] Univ Nantes, UMR CNRS 6004, LS2N, Nantes - France

• Tipo de documento: Artigo Científico
• Fonte: THEORETICAL COMPUTER SCIENCE; v. 715, p. 35-59, MAR 8 2018.
• Citações Web of Science: 0

Resumo

Comparative genomics is a line of study which aims at determining dis/similarities between genomes. One way of doing this is to infer the large scale mutations (also called genome rearrangements) that are responsible for transforming one genome into another, under the parsimony principle. Numerous efforts have been made over the past years regarding the traditional approach, in which all genome rearrangements have the same unit cost. However, since long rearrangements are more likely to disturb the organism, some works considered the length-weighted approach, in which the cost of each rearrangement is a function of its length. The problem is thus modeled as follows: given two genomes G(1) and G(2) and a set beta of allowed genome rearrangements, each with a given cost, determine their distance, i.e., the total cost of a minimum-cost sequence of rearrangements from beta that transforms G(1) into G(2). In this paper, we study length-weighted reversals and transpositions, mainly considering their prefix variants (in which the leftmost part of the genome must always be included). We present approximation algorithms and bounds on the distances and diameters (i.e., maximum possible distance over any two genomes of same length) for eight problems when genomes are represented as permutations, and another eight problems when genomes are represented as binary strings, in each case considering two different cost functions. (C) 2018 Elsevier B.V. All rights reserved. (AU)

• Processo FAPESP: 14/20738-7 - Ordenação de permutações por reversões de prefixo e reversões de sufixo
• Beneficiário: Carla Negri Lintzmayer
• Linha de fomento: Bolsas no Exterior - Estágio de Pesquisa - Doutorado Direto
• Processo FAPESP: 14/19401-8 - Algoritmos para rearranjos de genomas
• Beneficiário: Zanoni Dias
• Linha de fomento: Auxílio à Pesquisa - Regular
• Processo FAPESP: 13/01172-0 - O problema da ordenação de permutações usando operações de prefixo e sufixo
• Beneficiário: Carla Negri Lintzmayer
• Linha de fomento: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 15/11937-9 - Investigação de problemas difíceis do ponto de vista algorítmico e estrutural
• Beneficiário: Flávio Keidi Miyazawa
• Linha de fomento: Auxílio à Pesquisa - Temático
• 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