An efficient numerical representation of genome sequence: natural vector with covariance component

PeerJ

article

Nan Sun¹  Xin Zhao²  Stephen S.-T. Yau¹ 

[1] Department of Mathematical Sciences, Tsinghua University;Beijing Electronic Science and Technology Institute;Yanqi Lake Beijing Institute of Mathematical Sciences and Applications

关键词: Bacteria;    Virus;    Giant virus;    Archaea;    Fungi;    Convex hull classification;    The nearest neighbor classification;    Phylogeny;    Natural vector with covariance component;   

DOI  :  10.7717/peerj.13544

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background The characterization and comparison of microbial sequences, including archaea, bacteria, viruses and fungi, are very important to understand their evolutionary origin and the population relationship. Most methods are limited by the sequence length and lack of generality. The purpose of this study is to propose a general characterization method, and to study the classification and phylogeny of the existing datasets. Methods We present a new alignment-free method to represent and compare biological sequences. By adding the covariance between each two nucleotides, the new 18-dimensional natural vector successfully describes 24,250 genomic sequences and 95,542 DNA barcode sequences. The new numerical representation is used to study the classification and phylogenetic relationship of microbial sequences. Results First, the classification results validate that the six-dimensional covariance vector is necessary to characterize sequences. Then, the 18-dimensional natural vector is further used to conduct the similarity relationship between giant virus and archaea, bacteria, other viruses. The nearest distance calculation results reflect that the giant viruses are closer to bacteria in distribution of four nucleotides. The phylogenetic relationships of the three representative families, Mimiviridae, Pandoraviridae and Marsellieviridae from giant viruses are analyzed. The trees show that ten sequences of Mimiviridae are clustered with Pandoraviridae, and Mimiviridae is closer to the root of the tree than Marsellieviridae. The new developed alignment-free method can be computed very fast, which provides an effective numerical representation for the sequence of microorganisms.

【 授权许可】

CC BY