| Full text | |
| Author(s): |
Brito, Klairton Lima
[1]
;
Jean, Geraldine
[2]
;
Fertin, Guillaume
[2]
;
Oliveira, Andre Rodrigues
[1]
;
Dias, Ulisses
[3]
;
Dias, Zanoni
[1]
Total Authors: 6
|
| Affiliation: | [1] Univ Estadual Campinas, Inst Comp, 1251 Albert Einstein Ave, BR-13083852 Campinas, SP - Brazil
[2] Univ Nantes, LS2N UMR CNRS 6004, Nantes - France
[3] Univ Estadual Campinas, Sch Technol, Limeira - Brazil
Total Affiliations: 3
|
| Document type: | Journal article |
| Source: | JOURNAL OF COMPUTATIONAL BIOLOGY; v. 27, n. 2 DEC 2019. |
| Web of Science Citations: | 0 |
| Abstract | |
During the evolutionary process, genomes are affected by various genome rearrangements, that is, events that modify large stretches of the genetic material. In the literature, a large number of models have been proposed to estimate the number of events that occurred during evolution; most of them represent a genome as an ordered sequence of genes, and, in particular, disregard the genetic material between consecutive genes. However, recent studies showed that taking into account the genetic material between consecutive genes can enhance evolutionary distance estimations. Reversal and transposition are genome rearrangements that have been widely studied in the literature. A reversal inverts a (contiguous) segment of the genome, while a transposition swaps the positions of two consecutive segments. Genomes also undergo nonconservative events (events that alter the amount of genetic material) such as insertions and deletions, in which genetic material from intergenic regions of the genome is inserted or deleted, respectively. In this article, we study a genome rearrangement model that considers both gene order and sizes of intergenic regions. We investigate the reversal distance, and also the reversal and transposition distance between two genomes in two scenarios: with and without nonconservative events. We show that these problems are NP-hard and we present constant ratio approximation algorithms for all of them. More precisely, we provide a 4-approximation algorithm for the reversal distance, both in the conservative and nonconservative versions. For the reversal and transposition distance, we provide a 4.5-approximation algorithm, both in the conservative and nonconservative versions. We also perform experimental tests to verify the behavior of our algorithms, as well as to compare the practical and theoretical results. We finally extend our study to scenarios in which events have different costs, and we present constant ratio approximation algorithms for each scenario. (AU) | |
| FAPESP's process: | 17/12646-3 - Déjà vu: feature-space-time coherence from heterogeneous data for media integrity analytics and interpretation of events |
| Grantee: | Anderson de Rezende Rocha |
| Support Opportunities: | Research Projects - Thematic Grants |
| FAPESP's process: | 17/16246-0 - Sensitive media analysis through deep learning architectures |
| Grantee: | Sandra Eliza Fontes de Avila |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 15/11937-9 - Investigation of hard problems from the algorithmic and structural stand points |
| Grantee: | Flávio Keidi Miyazawa |
| Support Opportunities: | Research Projects - Thematic Grants |