Periodic correlation structures in bacterial and archaeal complete genomes

TL;DR

This paper investigates the periodic transfer of nucleotide strings in bacterial and archaeal genomes using metric representation and recurrence plots, revealing four fundamental transfer patterns and explaining their mechanisms.

Contribution

It introduces a novel analysis of periodic correlation structures in genomes, identifying four key transfer characteristics and elucidating their underlying mechanisms.

Findings

Identification of four types of periodic transfer patterns

Repetition and transference of nucleotide strings explain correlation structures

Mechanistic insight into genome periodicity phenomena

Abstract

The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds of fundamental transferring characteristics: a single increasing period, several increasing periods, an increasing quasi-period and almost noincreasing period. The mechanism of the periodic transference is further analyzed by determining all long periodic nucleotide strings in the bacterial and archaeal complete genomes and is explained as follows: both the repetition of basic periodic nucleotide strings and the transference of non-periodic nucleotide strings would form the periodic correlation structures with approximately the same increasing periods.