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(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.)

On the Complexity of Some Variations of Sorting by Transpositions

Autor(es):
Alexandrino, Alexsandro Oliveira [1] ; Oliveira, Andre Rodrigues [1] ; Dias, Ulisses [2] ; Dias, Zanoni [1]
Número total de Autores: 4
Afiliação do(s) autor(es):
[1] Univ Estadual Campinas, Inst Comp, Campinas, SP - Brazil
[2] Univ Estadual Campinas, Sch Technol, Limeira, SP - Brazil
Número total de Afiliações: 2
Tipo de documento: Artigo Científico
Fonte: JOURNAL OF UNIVERSAL COMPUTER SCIENCE; v. 26, n. 9, p. 1076-1094, 2020.
Citações Web of Science: 0
Resumo

One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements (large scale mutations) needed to transform one genome into another, which is called the rearrangement distance. In the past decades, these problems were studied considering many types of rearrangements (such as reversals, transpositions, transreversals, and revrevs) and considering the same weight for all rearrangements, or different weights depending on the types of rearrangements. The complexity of the problems involving reversals, transpositions, and both rearrangements is known, even though the hardness proof for the problem combining reversals and transpositions was recently given. In this paper, we enhance the knowledge for these problems by proving that models involving transpositions alongside reversals, transreversals, and revrevs are NP-hard, considering weights w(1) for reversals and w(2) for the other rearrangements such that w(2)/w(1) <= 1.5. In addition, we address a cost function related to the number of fragmentations caused by a rearrangement, proving that the problem of finding a minimum cost sorting sequence, considering the fragmentation cost function with some restrictions, is NP-hard for transpositions and the combination of reversals and transpositions. (AU)

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
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: 19/27331-3 - Problemas de ordenação por rearranjos de genomas
Beneficiário:André Rodrigues Oliveira
Linha de fomento: Bolsas no Brasil - Pós-Doutorado
Processo FAPESP: 17/12646-3 - Déjà vu: coerência temporal, espacial e de caracterização de dados heterogêneos para análise e interpretação de integridade
Beneficiário:Anderson de Rezende Rocha
Linha de fomento: Auxílio à Pesquisa - Temático