Sorting permutations by prefix reversals and suffix reversals
The sorting permutations problem using prefix and suffix operations
Metabolism and B lymphocytes: effects of caloric restriction on the mitochondrial ...
| Full text | |
| Author(s): |
Brito, Klairton Lima
;
Alexandrino, Alexsandro Oliveira
;
Oliveira, Andre Rodrigues
;
Dias, Ulisses
;
Dias, Zanoni
;
Setubal, JC
;
Silva, WM
Total Authors: 7
|
| Document type: | Journal article |
| Source: | ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, BSB 2020; v. 12558, p. 12-pg., 2020-01-01. |
| 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 more 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 present an approximation algorithm applicable to any desired proportion, for both scenarios where the orientation of the genes is known or unknown. We also show an improved (asymptotic) approximation algorithm for the case where the gene orientation is known. (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: | 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: | 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: | 15/11937-9 - Investigation of hard problems from the algorithmic and structural stand points |
| Grantee: | Flávio Keidi Miyazawa |
| Support Opportunities: | Research Projects - Thematic Grants |