Periodic Correlation Structures in Bacterial and Archaeal Complete Genomes

Zuo-Bing      Wu

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.

Keywords: Bacterial and archaeal complete genomes, periodic correlation structures, metric representation, recurrence plots, synecho genome, Mycobacterium tuberculosis, symbolic dynamics, organisms, nucleotide strings