A general heuristic for genome rearrangement problems

Journal of Bioinformatics and Computational Biology
Ulisses DiasZanoni Dias

Abstract

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 pr...Continue Reading

References

Feb 17, 2017·Journal of Bioinformatics and Computational Biology·Carla Negri LintzmayerZanoni Dias

Citations

Nov 7, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Isaac Elias, Tzvika Hartman
Nov 1, 2007·Academic Medicine : Journal of the Association of American Medical Colleges·Andrew H Brainard, Heather C Brislen
Oct 18, 2013·Journal of Bioinformatics and Computational Biology·Ulisses Dias, Zanoni Dias

Related Concepts

Sequence Inversion
Heuristics
Cellular Transposition
Sorting - Cell Movement
Congenital Transposition
Suffix brand of benzoylprop-ethyl
DNA Sequence Rearrangement
Gene Rearrangement
Online Mendelian Inheritance In Man
Computational Molecular Biology

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