Sorting permutations by prefix reversals and suffix reversals
Problems of sorting permutations by fragmentation-weighted operations
The sorting permutations problem using prefix and suffix operations
| Author(s): |
Total Authors: 3
|
| Affiliation: | [1] Univ Estadual Campinas, Inst Comp, Campinas, SP - Brazil
[2] Fed Univ ABC, Ctr Math Computat & Cognit, Santo Andre - Brazil
Total Affiliations: 2
|
| Document type: | Journal article |
| Source: | JOURNAL OF UNIVERSAL COMPUTER SCIENCE; v. 25, n. 2, p. 98-121, 2019. |
| Web of Science Citations: | 0 |
| Abstract | |
For estimating the evolutionary distance between genomes of two different organisms, many sorting permutation problems have emerged. A well accepted way to do this is considering the smallest sequence of rearrangement events - mutations which affect large portions of the genomes - that transform one genome into the other. In these problems, both genomes are represented as permutations of integer numbers, but one of them can be represented as the identity permutation, so that the problem is reduced to sort a permutation. Moreover, rearrangement models define which type of operations (rearrangement events) can be applied over a permutation in order to modify it. Reversals, which are operations that revert a genome segment, and transpositions, which are operations that swap two adjacent genome segments, are two of the most studied types of rearrangements in the literature. In this paper, we consider rearrangement models that allow reversals, transpositions, and both operations together. Since there exist evidences that large mutations rarely occur, we add a restriction with biological relevance: any operation can affect at most lambda elements of a permutation. For this variation of sorting permutation problem, we present approximation algorithms with approximation factors based on the size of the permutation and/or on lambda, for both signed and unsigned permutations (which represent known and unknown gene orientations, respectively). (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: | 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: | 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: | 16/14132-4 - One and two-dimensional bin packing with conflicts and unloading restrictions |
| Grantee: | Carla Negri Lintzmayer |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |