Four Basic Symmetry Types in the Universal 7-Cluster Structure of Microbial Genomic Sequences

Article type: Research Article

Authors: Gorban, Alexander N.^; | Popova, Tatyana G. | Zinovyev, Andrei Y.^;

Affiliations: Institute of Computational Modeling, Russian Academy of Science, Russia | Centre for Mathematical Modelling, University of Leicester, UK | Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette, France | Service Bioinformatique, Institut Curie, Paris, France

Note: [] Corresponding author. E-mail: andrei.zinovyev@curie.fr

Abstract: Coding information is the main source of heterogeneity (non-randomness) in the sequences of microbial genomes. The heterogeneity corresponds to a cluster structure in triplet distributions of relatively short genomic fragments (200–400 bp). We found a universal 7-cluster structure in microbial genomic sequences and explained its properties. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy. Based on the analysis of 143 completely sequenced bacterial genomes available in Genbank in August 2004, we show that there are four "pure" types of the 7-cluster structure observed. All 143 cluster animated 3D-scatters are collected in a database which is made available on our web-site (http://www.ihes.fr/~zinovyev/7clusters). The findings can be readily introduced into software for gene prediction, sequence alignment or microbial genomes classification.

Keywords: word frequency, codon usage, clustering, visualization, symmetry

Journal: In Silico Biology, vol. 5, no. 3, pp. 265-282, 2005