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
;
Ferreira, CE
;
Lee, O
;
Miyazawa, FK
Total Authors: 8
|
| Document type: | Journal article |
| Source: | PROCEEDINGS OF THE XI LATIN AND AMERICAN ALGORITHMS, GRAPHS AND OPTIMIZATION SYMPOSIUM; v. 195, p. 9-pg., 2021-01-01. |
| Abstract | |
Biologists have proposed a vast list of problems heavily studied by mathematicians, computer scientists, and statisticians. From a theoretical point of view, biology can inspire exciting new problems when one is interested in estimating genetic modifications that occurred in the course of evolution. Structural modifications, such as genome rearrangements, are important for comparative genomics and they have led to many NP-hard problems. Reversal and Transposition are the most studied genome rearrangement events. To solve these problems, the gene order inside a genome is usually mapped into a permutation or a string. Permutations do not allow us to work with duplicate genes; in this case strings should be used. Problems with reversals and transpositions on permutations and strings are being studied since the 70s. Recently, studies start incorporating information regarding the size of the intergenic regions, which are genetic regions between each pair of consecutive genes inside the genome with a specific number of nucleotides. Problems can differ by changing the genetic information carried into the representation model, but all of them aim to transform a source genome into a target genome. In this work, we study the Sorting by Reversals with Flexible Intergenic Regions and Sorting by Reversals and Transpositions with Flexible Intergenic Regions problems on unsigned permutations. The goal is still to transform a source genome into the target genome, but turning the constraint less strict regarding the size of the intergenic regions on the target genome. We present a theoretical study showing that both problems are NP -hard and algorithms with constant approximation factor. (C) 2021 The Authors. Published by Elsevier B.V. (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: | 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 |
| 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 |