Title
Computing translocation distance by a genetic algorithm
Date Issued
16 December 2015
Access level
open access
Resource Type
conference paper
Author(s)
Da Silveira L.
De Lima T.
Ayala-Rincon M.
Universidade de Brasília
Publisher(s)
Institute of Electrical and Electronics Engineers Inc.
Abstract
Translocation is a useful operation on strings with challenging questions in combinatorics of permutations and interesting applications in analysis of sequences. A translocation operation essentially is the interchange of prefixes and suffixes among two substrings of a string. For the case of genomes represented as strings, symbols that represent genes and chromosomes are modeled as substrings of the genomes; thus, translocation is an operation that models the interaction between chromosomes inside a genome. The translocation distance between two genomes is defined as the minimum number of translocations to convert one genome into another and has been proved to be a meaningful manner of modeling the evolutive distance between organisms. The particular case of unsigned genomes, those in which the orientation of the genes are not considered, is particularly difficult, while the signed case, in which the orientation of genes is considered, has been proved to be polynomially decidable. This paper presents an innovative Genetic Algorithm (GA) approach to solve the unsigned translocation distance problem. A distinguishing feature of the proposed GA is that it uses as fitness function the translocation distance for randomly generated signed versions of the input (that is an unsigned genome). Experiments over randomly generated strings (synthetic genomes) showed that the proposed GA approach computes answers that are better than those computed by an L5+ε-approximation algorithm, the latter also implemented as part of this work.
Language
English
OCDE Knowledge area
Bioinformática
Scopus EID
2-s2.0-84961967613
ISBN of the container
978-146739143-6
Conference
Proceedings - 2015 41st Latin American Computing Conference, CLEI 2015
Sources of information: Directorio de Producción Científica Scopus