K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

• Published in: Gene Vol. 546; no. 1; pp. 25 - 34
• Main Authors: Wen, Jia, Chan, Raymond H.F., Yau, Shek-Chung, He, Rong L., Yau, Stephen S.T.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2014
• Subjects: Algorithms; Animals; DNA, Mitochondrial; Evolution, Molecular; Genetic Vectors; Genome; Genome, Human; Humans; K-mer model; Mammals - genetics; Mitochondria - genetics; Models, Genetic; Natural vector; Phylogenetic analysis; Phylogeny; Sequence Analysis, DNA - methods; Phylogenetic analysis; A; C; UPGMA; T; G; K-mer model; Natural vector; NJ; bp
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.05.043

Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency. •A one-to-one correspondence between genetic sequence and its k-mer natural vector•Phylogenetic analysis does not need any evolutionary model or human intervention.•Whole or partial genomes can be handled more effectively with our proposed method.•Our method is a very powerful tool for analysing and annotating genetic sequences.