| Texto completo | |
| Autor(es): |
Brito, Klairton Lima
[1]
;
Alexandrino, Alexsandro Oliveira
[1]
;
Oliveira, Andre Rodrigues
[1]
;
Dias, Ulisses
[2]
;
Dias, Zanoni
[1]
Número total de Autores: 5
|
| Afiliação do(s) autor(es): | [1] Univ Estadual Campinas, Inst Comp, 1251 Albert Einstein Ave, BR-13083852 Campinas, SP - Brazil
[2] Univ Estadual Campinas, Sch Technol, 1888 Paschoal Marmo St, BR-13484332 Limeira, SP - Brazil
Número total de Afiliações: 2
|
| Tipo de documento: | Artigo Científico |
| Fonte: | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. 19, n. 4 AUG 2021. |
| Citações Web of Science: | 0 |
| Resumo | |
In the field of comparative genomics, one way of comparing two genomes is through the analysis of how they distinguish themselves based on a set of mutations called rearrangement events. When considering that genomes undergo different types of rearrangements, it can be assumed that some events are more common than others. To model this assumption, one can assign different weights to different events, where common events tend to cost less than others. However, this approach, called weighted, does not guarantee that the rearrangement assumed to be the most frequent will be also the most frequently returned by proposed algorithms. To overcome this issue, we investigate a new problem where we seek the shortest sequence of rearrangement events able to transform one genome into the other, with a restriction regarding the proportion between the events returned. Here, we consider two rearrangement events: reversal, that inverts the order and the orientation of the genes inside a segment of the genome, and transposition, that moves a segment of the genome to another position. We show the complexity of this problem for any desired proportion considering scenarios where the orientation of the genes is known or unknown. We also develop an approximation algorithm with a constant approximation factor for each scenario and, in particular, we describe an improved (asymptotic) approximation algorithm for the case where the gene orientation is known. At last, we present the experimental tests comparing the proposed algorithms with others from the literature for the version of the problem without the proportion restriction. (AU) | |
| Processo FAPESP: | 19/27331-3 - Problemas de ordenação por rearranjos de genomas |
| Beneficiário: | André Rodrigues Oliveira |
| Modalidade de apoio: | 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 |
| Modalidade de apoio: | Auxílio à Pesquisa - Temático |
| 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: | 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais |
| Beneficiário: | Munir Salomao Skaf |
| Modalidade de apoio: | 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 |
| Modalidade de apoio: | Auxílio à Pesquisa - Temático |