Genomes are covered with ubiquitous 11bp periodic patterns, the "class A flexible patterns"

Abstract

Background: The genomes of prokaryotes and lower eukaryotes display a very strong 11bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin. Results: Using a technique for analysis of auto-correlations based on linear projection, we identified the sequences responsible for the bias. Prokaryotic and lower eukaryotic genomes are covered with ubiquitous patterns that we termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50bp in length. They belong to what we named the "flexible pattern" type, in that there is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11bp periodic bias. Conclusions: Judging from the structure of the patterns, we suggest that they may define a dense network of protein interaction sites in chromosomes. © 2005 Larsabal and Danchin, licensee BioMed Central Ltd.