Molecular Biology and Evolution, Vol 16, 1391-1399, Copyright © 1999 by Society for Molecular Biology and Evolution
PJ Deschavanne, A Giron, J Vilain, G Fagot and B Fertil
We explored DNA structures of genomes by means of a new tool derived from
the "chaotic dynamical systems" theory (the so-called chaos game
representation [CGR]), which allows the depiction of frequencies of
oligonucleotides in the form of images. Using CGR, we observe that
subsequences of a genome exhibit the main characteristics of the whole
genome, attesting to the validity of the genomic signature concept. Base
concentrations, stretches (runs of complementary bases or
purines/pyrimidines), and patches (over- or underexpressed words of various
lengths) are the main factors explaining the variability observed among
sequences. The distance between images may be considered a measure of
phylogenetic proximity. Eukaryotes and prokaryotes can be identified merely
on the basis of their DNA structures.
ORIGINAL ARTICLE
Genomic signature: characterization and classification of species assessed by chaos game representation of sequences
Laboratoire de Mutagenese, Institut Jacques Monod, Paris, France. deschavanne@imed.jussieu.fr
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