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Mol Biol Evol. 1999 Oct;16(10):1391-9.

Genomic signature: characterization and classification of species assessed by chaos game representation of sequences.

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  • 1Laboratoire de Mutagénèse, Institut Jacques Monod, Paris, France. deschavanne@imed.jussieu.fr

Abstract

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.

PMID:
10563018
[PubMed - indexed for MEDLINE]
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