| Full text | |
| Author(s): |
Siqueira, Gabriel
;
Oliveira, Andre Rodrigues
;
Alexandrino, Alexsandro Oliveira
;
Dias, Zanoni
;
Stadler, PF
;
Walter, MEMT
;
Hernandez-Rosales, M
;
Brigido, MM
Total Authors: 8
|
| Document type: | Journal article |
| Source: | ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, BSB 2021; v. 13063, p. 13-pg., 2021-01-01. |
| Abstract | |
The Adjacency Graph is a structure used to model genomes in several rearrangement distance problems. In particular, most studies use properties of a maximum cycle packing of this graph to develop bounds and algorithms for rearrangement distance problems, such as the reversal distance and the Double Cut and Join (DCJ) distance. When each genome has no repeated genes, there exists only one cycle packing for the graph. However, when each genome may have repeated genes, the problem of finding a maximum cycle packing for the adjacency graph (Adjacency Graph Packing) is NP-hard. In this work, we developed a greedy random heuristic and a genetic algorithm heuristic for the Adjacency Graph Packing problem for genomes with repeated genes. We present experimental results and compare these heuristics with the SOAR framework. Furthermore, we show how the solutions from our algorithms can improve the estimation for the reversal distance when compared to the SOAR framework. Lastly, we applied our genetic algorithm heuristic in real genomic data to validate its practical use. (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: | 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 |