Sorting permutations by prefix reversals and suffix reversals
The sorting permutations problem using prefix and suffix operations
| Full text | |
| Author(s): |
Brito, Klairton Lima
[1]
;
Alexandrino, Alexsandro Oliveira
[1]
;
Oliveira, Andre Rodrigues
[1]
;
Dias, Ulisses
[2]
;
Dias, Zanoni
[1]
Total Authors: 5
|
| Affiliation: | [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
Total Affiliations: 2
|
| Document type: | Journal article |
| Source: | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. 19, n. 4 AUG 2021. |
| Web of Science Citations: | 0 |
| Abstract | |
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) | |
| FAPESP's process: | 19/27331-3 - Sorting by genome rearrangements problems |
| Grantee: | André Rodrigues Oliveira |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| 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: | 13/08293-7 - CCES - Center for Computational Engineering and Sciences |
| Grantee: | Munir Salomao Skaf |
| Support Opportunities: | Research Grants - Research, Innovation and Dissemination Centers - RIDC |
| 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 |