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

Abstract

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.

Keywords: K-mer model; Natural vector; Phylogenetic analysis.

Figure 1

Phylogenetic tree of 31 mitochondrial genome sequences based on 9-mer natural vector. All 31 genomes are correctly clustered into eight known clusters: Carnivora (red), Perissodactyla (blue), Artiodactyla (yellow), Cetacea (light green), Lagomorpha (light blue), Rodentia (purple), Primates (green) and Erinaceomorpha (light green), which agrees with results from standard biological taxonomy and evolutionary relationships of species.

Figure 2

Phylogenetic tree of 31 mitochondrial genome sequences obtained by multiple sequence alignment (clustalW).

Figure 3

Phylogenetic tree of 53 human mitochondrial genome sequences based on 8-mer natural vector. The 53 mtDNAs are mainly divided into two parts: non-Africans (red and green) and Africans (blue, yellow, brown and purple), and humans in each group correctly cluster, which is consistent with known evidences of human evolution and human migration.

Figure 4

Phylogenetic tree of 53 human mitochondrial genome sequences obtained by multiple sequence alignment (clustalW).

Figure 5

Phylogenetic tree of 40 18S rRNA sequences based on 6-mer natural vector. The phylogenetic tree of 18S rRNAs contains four clades: Birds (green), Crocodilians (blue), Mammals (red) and Amphibians (purple), and the species in each clade correctly group together that conform to results from traditional classification.

Figure 6

Phylogenetic tree of 40 18S rRNA sequences obtained by multiple sequence alignment (clustalW).