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

ABSTRACT:

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

SUBMITTER: Sun N 

PROVIDER: S-EPMC9206847 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature