Pervasive properties of the genomic signature

Abstract

Background: The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the causes and the functional significance of this phenomenon could be illuminated by determining if it persists on smaller scales. The profile is computed from the base step "odds ratios" that compare dinucleotide frequencies to those expected under the assumption of stochastic equilibrium (thorough shuffling). Analysis is carried out on 22 sequences, representing 19 species and comprised of about 53 million bases all together, to assess stability of the signature in windows ranging in size from 50 kilobases down to 125 bases. Results: Dinucleotide relative abundance distance from the global signature is computed locally for all non-overlapping windows on each sequence. These distances are log-normally distributed with nearly constant variance and with means that tend to zero slower than reciprocal square root of window size. The mean distance within genomes is larger for protist, plant, and human chromosomes, and smaller for archaea, bacteria, and yeast, for any window size. Conclusions: The imprint of the global signature is locally pervasive on all scales considered in the sequences (either genomes or chromosomes) that were scanned. © 2002 Jernigan and Bara; licensee BioMed Central Ltd.