| Full text | |
| Author(s): |
Alexandrino, Alexsandro Oliveira
;
Oliveira, Andre Rodrigues
;
Jean, Geraldine
;
Fertin, Guillaume
;
Dias, Ulisses
;
Dias, Zanoni
Total Authors: 6
|
| Document type: | Journal article |
| Source: | JOURNAL OF COMPUTATIONAL BIOLOGY; v. 30, n. 8, p. 16-pg., 2023-05-24. |
| Abstract | |
The most common way to calculate the rearrangement distance between two genomes is to use the size of a minimum length sequence of rearrangements that transforms one of the two given genomes into the other, where the genomes are represented as permutations using only their gene order, based on the assumption that genomes have the same gene content. With the advance of research in genome rearrangements, new works extended the classical models by either considering genomes with different gene content (unbalanced genomes) or including more genomic characteristics to the mathematical representation of the genomes, such as the distribution of intergenic regions sizes. In this study, we study the Reversal, Transposition, and Indel (Insertion and Deletion) Distance using intergenic information, which allows comparing unbalanced genomes, because indels are included in the rearrangement model (i.e., the set of possible rearrangements allowed when we compute the distance). For the particular case of transpositions and indels on unbalanced genomes, we present a 4-approximation algorithm, improving a previous 4.5 approximation. This algorithm is extended so as to deal with gene orientation and to maintain the 4-approximation factor for the Reversal, Transposition, and Indel Distance on unbalanced genomes. Furthermore, we evaluate the proposed algorithms using experiments on simulated data. (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 |