GDL

Journal from gdlhub / 2018-11-28 09:46:20
By : Arini Pekuwali, Wisnu Ananta Kusuma, Agus Buono, ITB
Created : 2018-11-28, with 1 files

Keyword : genetic algorithm; k-mers; metagenome; naïve Bayesian classifier; spaced k-mers
Url : http://journals.itb.ac.id/index.php/jictra/article/view/3228
Document Source : WEB

K-mer frequencies are commonly used in extracting features from metagenome fragments. In spite of this, researchers have found that their use is still inefficient. In this research, a genetic algorithm was employed to find optimally spaced k-mers. These were obtained by generating the possible combinations of match positions and don’t care positions (written as *). This approach was adopted from the concept of spaced seeds in PatternHunter. The use of spaced k-mers could reduce the size of the k-mer frequency feature’s dimension. To measure the accuracy of the proposed method we used the naïve Bayesian classifier (NBC). The result showed that the chromosome 111111110001, representing spaced k-mer model [111 1111 10001], was the best chromosome, with a higher fitness (85.42) than that of the k-mer frequency feature. Moreover, the proposed approach also reduced the feature extraction time.

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