Rearrangement distances in unbalanced genomes considering intergenic regions
Sorting permutations by prefix reversals and suffix reversals
The sorting permutations problem using prefix and suffix operations
| Full text | |
| Author(s): |
Brito, Klairton Lima
;
Oliveira, Andre Rodrigues
;
Alexandrino, Alexsandro Oliveira
;
Dias, Ulisses
;
Dias, Zanoni
Total Authors: 5
|
| Document type: | Journal article |
| Source: | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. N/A, p. 30-pg., 2023-04-27. |
| Abstract | |
Genome rearrangement events are widely used to estimate a minimum-size sequence of mutations capable of transforming a genome into another. The length of this sequence is called distance, and determining it is the main goal in genome rearrangement distance problems. Problems in the genome rearrangement field differ regarding the set of rearrangement events allowed and the genome representation. In this work, we consider the scenario where the genomes share the same set of genes, gene orientation is known or unknown, and intergenic regions (structures between a pair of genes and at the extremities of the genome) are taken into account. We use two models, the first model allows only conservative events (reversals and moves), and the second model includes non-conservative events (insertions and deletions) in the intergenic regions. We show that both models result in NP-hard problems no matter if gene orientation is known or unknown. When the information regarding the orientation of genes is available, we present for both models an approximation algorithm with a factor of 2. For the scenario where this information is unavailable, we propose a 4-approximation algorithm for both models. (AU) | |
| 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: | 19/27331-3 - Sorting by genome rearrangements problems |
| Grantee: | André Rodrigues Oliveira |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| 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 |