Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation

International Journal of Online and Biomedical Engineering

Vijini Mallawaarachchi¹  Anuradha Wickramarachchi¹  Indika Perera²  Nadeeshan Gimhana³  Gihan Gamage³  Thilina Pathirana³  Shanaka Bandara³ 

[1] Australian National University, Australia.;University of Moratuwa, Srilanka.;University of Moratuwa, Srilanka;

关键词: phylogenetics;    genetic relatedness;    genetic distance;    k-mer forest;    k-medoid clustering;   

DOI  :  10.3991/ijoe.v16i07.13807

来源: DOAJ

【 摘 要 】

Phylogenetics is one of the dominant data engineering research disciplines based on biological information. More particularly here, we consider raw DNA sequences and do comparative analysis in order to come up with important conclusions. When representing evolutionary relationships among different organisms in a concise manner, the phylogenetic tree helps significantly. When constructing phylogenetic trees, the elementary step is to calculate the genetic distance among species. Alignment-based sequencing and alignment-free sequencing are the two main distance computation methods that are used to find genetic relatedness of different species. In this paper we propose a novel alignment-free, pairwise, distance calculation method based on k-mers and a state of art machine learning-based phylogenetic tree construction mechanism. With the proposed approach we can convert longer DNA sequences into compendious k-mer forests which gear up the efficiency of comparison. Later we construct the phylogenetic tree based on calculated distances with the help of an algorithm build upon k-medoid clustering, which guaranteed significant efficiency and accuracy compared to traditional phylogenetic tree construction methods.

【 授权许可】

Unknown