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Selection of a minimal number of significant porcine snps by an information gain and genetic algorithm hybrid model
Author(s)
Date Issued
January 1, 2019
Type
Article
Abstract
A panel of a large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pigs. With the advent of SNP-array technology, a genome-wide genetic profile of a specimen can be easily observed. Among the large number of such variations, there exists a much smaller subset of the SNP panel that could equally be used to correctly identify the corresponding breed. This work presents a SNP selection heuristic that can still be used effectively in the breed classification. The features were selected by combining a filter method and a wrapper method-information gain method and genetic algorithm-plus a feature frequency selection step, while classification used a support vector machine. We were able to reduce the number of significant SNPs to 0.86 % of the total number of SNPs in a swine dataset with 94.80 % classification accuracy.
Citation
Malaysian Journal of Computer Science, 2019(SpecialIssue2), 79-95, 2019