Problems of sorting permutations by fragmentation-weighted operations
The sorting permutations problem using prefix and suffix operations
Sorting permutations by prefix reversals and suffix reversals
| Full text | |
| Author(s): |
Total Authors: 3
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| Affiliation: | [1] Univ Estadual Campinas, Inst Comp, UNICAMP, BR-13083852 Campinas, SP - Brazil
[2] Fed Univ ABC UFABC, Ctr Math Computat & Cognit, BR-09210580 Santo Andre, SP - Brazil
Total Affiliations: 2
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| Document type: | Journal article |
| Source: | JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. 18, n. 2 APR 2020. |
| Web of Science Citations: | 0 |
| Abstract | |
One of the main problems in Computational Biology is to find the evolutionary distance among species. In most approaches, such distance only involves rearrangements, which are mutations that alter large pieces of the species' genome. When we represent genomes as permutations, the problem of transforming one genome into another is equivalent to the problem of Sorting Permutations by Rearrangement Operations. The traditional approach is to consider that any rearrangement has the same probability to happen, and so, the goal is to find a minimum sequence of operations which sorts the permutation. However, studies have shown that some rearrangements are more likely to happen than others, and so a weighted approach is more realistic. In a weighted approach, the goal is to find a sequence which sorts the permutations, such that the cost of that sequence is minimum This work introduces a new type of cost function, which is related to the amount of fragmentation caused by a rearrangement. We present some results about the lower and upper bounds for the fragmentation-weighted problems and the relation between the unweighted and the fragmentation-weighted approach. Our main results are 2-approximation algorithms for five versions of this problem involving reversals and transpositions. We also give bounds for the diameters concerning these problems and provide an improved approximation factor for simple permutations considering transpositions. (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: | 17/16871-1 - Problems of sorting permutations by fragmentation-weighted operations |
| Grantee: | Alexsandro Oliveira Alexandrino |
| Support Opportunities: | Scholarships in Brazil - Master |
| FAPESP's process: | 17/16246-0 - Sensitive media analysis through deep learning architectures |
| Grantee: | Sandra Eliza Fontes de Avila |
| Support Opportunities: | Regular Research 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 |