sorting by reversals
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2020 ◽  
Author(s):  
Gustavo Rodrigues Galvão ◽  
Zanoni Dias

The problem of finding the minimum sequence of rearrangements that transforms one genome into another is a well-studied problem that finds application in comparative genomics. Representing genomes as permutations, in which genes appear as elements, that problem can be reduced to the combinatorial problem of sorting a permutation using a minimum number of rearrangements. Such combinatorial problem varies according to the types of rearrangements considered. The PhD thesis summarized in this paper presents exact, approximation, and heuristic algorithms for solving variants of the permutation sorting problem involving two types of rearrangements: reversals and transpositions.


Author(s):  
Klairton Lima Brito ◽  
Alexsandro Oliveira Alexandrino ◽  
Andre Rodrigues Oliveira ◽  
Ulisses Dias ◽  
Zanoni Dias
Keyword(s):  

2019 ◽  
Vol 26 (11) ◽  
pp. 1223-1229 ◽  
Author(s):  
Andre Rodrigues Oliveira ◽  
Klairton Lima Brito ◽  
Ulisses Dias ◽  
Zanoni Dias
Keyword(s):  

Author(s):  
Nayan Garg ◽  
Manubhav Jain ◽  
Sugandha Singhania ◽  
Parinay Prateek ◽  
Prantik Biswas ◽  
...  
Keyword(s):  

Author(s):  
Klairton Lima Brito ◽  
Géraldine Jean ◽  
Guillaume Fertin ◽  
Andre Rodrigues Oliveira ◽  
Ulisses Dias ◽  
...  

2018 ◽  
Vol 37 (4) ◽  
pp. 1170-1190
Author(s):  
Shanshan Zhai ◽  
Peng Zhang ◽  
Daming Zhu ◽  
Weitian Tong ◽  
Yao Xu ◽  
...  

2014 ◽  
Vol 12 (03) ◽  
pp. 1450012 ◽  
Author(s):  
Ulisses Dias ◽  
Gustavo Rodrigues Galvão ◽  
Carla Négri Lintzmayer ◽  
Zanoni Dias

In this paper, we present a general heuristic for several problems in the genome rearrangement field. Our heuristic does not solve any problem directly, it is rather used to improve the solutions provided by any non-optimal algorithm that solve them. Therefore, we have implemented several algorithms described in the literature and several algorithms developed by ourselves. As a whole, we implemented 23 algorithms for 9 well known problems in the genome rearrangement field. A total of 13 algorithms were implemented for problems that use the notions of prefix and suffix operations. In addition, we worked on 5 algorithms for the classic problem of sorting by transposition and we conclude the experiments by presenting results for 3 approximation algorithms for the sorting by reversals and transpositions problem and 2 approximation algorithms for the sorting by reversals problem. Another algorithm with better approximation ratio can be found for the last genome rearrangement problem, but it is purely theoretical with no practical implementation. The algorithms we implemented in addition to our heuristic lead to the best practical results in each case. In particular, we were able to improve results on the sorting by transpositions problem, which is a very special case because many efforts have been made to generate algorithms with good results in practice and some of these algorithms provide results that equal the optimum solutions in many cases. Our source codes and benchmarks are freely available upon request from the authors so that it will be easier to compare new approaches against our results.


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