title: 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.
authors.affiliation: School of Information Science, Suihua University, Suihua 152061, China; Department of Mathematics, The Chinese University of Hong Kong, Shatin 999077, Hong Kong.
authors.forename: Jia
authors.initials: J
authors.lastname: Wen
authors.affiliation: Department of Mathematics, The Chinese University of Hong Kong, Shatin 999077, Hong Kong.
authors.forename: Raymond H F
authors.initials: RH
authors.lastname: Chan
authors.affiliation: Information Technology Services Center, Hong Kong University of Science and Technology, Kowloon 999077, Hong Kong.
authors.forename: Shek-Chung
authors.initials: SC
authors.lastname: Yau
authors.affiliation: Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA.
authors.forename: Rong L
authors.initials: RL
authors.lastname: He
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China. Electronic address: yau@uic.edu.
authors.forename: Stephen S T
authors.initials: SS
authors.lastname: Yau
mesh_terms: D000465:Algorithms; D000818:Animals; D004272:DNA, Mitochondrial; D019143:Evolution, Molecular; D005822:Genetic Vectors; D016678:Genome; D015894:Genome, Human; D006801:Humans; D008322:Mammals / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004272:DNA, Mitochondrial
keywords: K-mer model; Natural vector; Phylogenetic analysis