Genomic signature: characterization and classification of species assessed by chaos game representation of sequences.
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.
Deschavanne
P J
PJ
Laboratoire de Mutagénèse, Institut Jacques Monod, Paris, France. deschavanne@imed.jussieu.fr
Giron
A
A
Vilain
J
J
Fagot
G
G
Fertil
B
B
D000465:Algorithms; D000818:Animals; D002965:Classification; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D007091:Image Processing, Computer-Assisted; D010802:Phylogeny; D013045:Species Specificity
D004247:DNA