Sorting permutations by fragmentation-weighted operations

Autor(es)

Alexandrino, Alexsandro Oliveira ^[1] ; Lintzmayer, Carla Negri ^[2] ; Dias, Zanoni ^[1]

Afiliação do(s) autor(es)

^[1] Univ Estadual Campinas, Inst Comp, UNICAMP, BR-13083852 Campinas, SP - Brazil

^[2] Fed Univ ABC UFABC, Ctr Math Computat & Cognit, BR-09210580 Santo Andre, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. 18, n. 2 APR 2020.
• Citações Web of Science: 0

Resumo

One of the main problems in Computational Biology is to find the evolutionary distance among species. In most approaches, such distance only involves rearrangements, which are mutations that alter large pieces of the species' genome. When we represent genomes as permutations, the problem of transforming one genome into another is equivalent to the problem of Sorting Permutations by Rearrangement Operations. The traditional approach is to consider that any rearrangement has the same probability to happen, and so, the goal is to find a minimum sequence of operations which sorts the permutation. However, studies have shown that some rearrangements are more likely to happen than others, and so a weighted approach is more realistic. In a weighted approach, the goal is to find a sequence which sorts the permutations, such that the cost of that sequence is minimum This work introduces a new type of cost function, which is related to the amount of fragmentation caused by a rearrangement. We present some results about the lower and upper bounds for the fragmentation-weighted problems and the relation between the unweighted and the fragmentation-weighted approach. Our main results are 2-approximation algorithms for five versions of this problem involving reversals and transpositions. We also give bounds for the diameters concerning these problems and provide an improved approximation factor for simple permutations considering transpositions. (AU)

• 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
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 17/16871-1 - Problemas de ordenação de permutações por operações ponderadas pelo número de fragmentações
• Beneficiário: Alexsandro Oliveira Alexandrino
• Modalidade de apoio: Bolsas no Brasil - Mestrado
• Processo FAPESP: 17/16246-0 - Análise de mídias sensíveis usando arquiteturas de aprendizado profundo
• Beneficiário: Sandra Eliza Fontes de Avila
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 15/11937-9 - Investigação de problemas difíceis do ponto de vista algorítmico e estrutural
• Beneficiário: Flávio Keidi Miyazawa
• Modalidade de apoio: Auxílio à Pesquisa - Temático