Title
Parallel memetic genetic algorithms for sorting unsigned genomes by translocations
Date Issued
14 November 2016
Access level
metadata only access
Resource Type
conference paper
Author(s)
Universidade de Brasília
Publisher(s)
Institute of Electrical and Electronics Engineers Inc.
Abstract
The rearrangement of genomes is an important tool for studying the evolution of genomes and specifically for the construction of phylogenies. A translocation splits and combines the strings of genes of a pair of chromosomes inside a genome and is considered a suitable operation for rearrangement of genomes with multiple chromosomes. The translocation distance between two genomes is the minimum number of translocations necessary to convert one of them into the other. Computing the translocation distance between two unsigned genomes, that is the case in which the direction of the genes between the chromosomes is not considered, is known to be an MV-hard optimization problem. Among several approximation algorithms that were proposed for solving this problem, the authors introduced in a previous work a genetic algorithm approach improved with opposition based learning and memetic mechanisms. In this paper, two parallel treatments of the sequential memetic approach are introduced for solving the translocation distance problem for unsigned genomes. The first approach, computes in parallel the fitness over all individuals of a population. This method intends speeding-up the sequential memetic algorithm. The second approach, processes in parallel multiple populations and was proposed for improving precision providing solutions with a less number of translocations than the sequential memetic algorithm. Several experiments were performed with randomly generated synthetic and biologically based genomes. Results show that the parallel approaches outperform the sequential memetic algorithm.
Start page
185
End page
192
Language
English
OCDE Knowledge area
Bioinformática
Subjects
Scopus EID
2-s2.0-85008263785
ISBN of the container
978-150900622-9
Conference
2016 IEEE Congress on Evolutionary Computation, CEC 2016
Sponsor(s)
The first two authors are funded by CAPES graduate scholarships and the third author by a CNPq grant.
Sources of information:
Directorio de Producción Científica
Scopus