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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. Kunin, A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz A Bioinformatician's Guide to Metagenomics Microbiol. Mol. Biol. Rev., December 1, 2008; 72(4): 557 - 578. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Martin, N. N. Diaz, J. Ontrup, and T. W. Nattkemper Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification Bioinformatics, July 15, 2008; 24(14): 1568 - 1574. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Reed, V. Fofanov, C. Putonti, S. Chumakov, T. Slezak, and Y. Fofanov Effect of the mutation rate and background size on the quality of pathogen identification Bioinformatics, October 15, 2007; 23(20): 2665 - 2671. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Shedlock, C. W. Botka, S. Zhao, J. Shetty, T. Zhang, J. S. Liu, P. J. Deschavanne, and S. V. Edwards Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome PNAS, February 20, 2007; 104(8): 2767 - 2772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Rosas-Magallanes, P. Deschavanne, L. Quintana-Murci, R. Brosch, B. Gicquel, and O. Neyrolles Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis Mol. Biol. Evol., June 1, 2006; 23(6): 1129 - 1135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P.-E. Fournier, K. Suhre, G. Fournous, and D. Raoult Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes. Int J Syst Evol Microbiol, May 1, 2006; 56(Pt 5): 1025 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. D'Auria, R. Pushker, and F. Rodriguez-Valera IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships Bioinformatics, March 1, 2006; 22(5): 527 - 531. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Ricke, M. Kube, S. Nakagawa, C. Erkel, R. Reinhardt, and W. Liesack First Genome Data from Uncultured Upland Soil Cluster Alpha Methanotrophs Provide Further Evidence for a Close Phylogenetic Relationship to Methylocapsa acidiphila B2 and for High-Affinity Methanotrophy Involving Particulate Methane Monooxygenase Appl. Envir. Microbiol., November 1, 2005; 71(11): 7472 - 7482. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Fertil, M. Massin, S. Lespinats, C. Devic, P. Dumee, and A. Giron GENSTYLE: exploration and analysis of DNA sequences with genomic signature Nucleic Acids Res., July 1, 2005; 33(suppl_2): W512 - W515. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Regeard, J. Maillard, C. Dufraigne, P. Deschavanne, and C. Holliger Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer by Dehalococcoides ethenogenes Strain 195 Appl. Envir. Microbiol., June 1, 2005; 71(6): 2955 - 2961. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Dufraigne, B. Fertil, S. Lespinats, A. Giron, and P. Deschavanne Detection and characterization of horizontal transfers in prokaryotes using genomic signature Nucleic Acids Res., January 13, 2005; 33(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. W. Hahn, J. E. Stajich, and G. A. Wray The Effects of Selection Against Spurious Transcription Factor Binding Sites Mol. Biol. Evol., June 1, 2003; 20(6): 901 - 906. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Sandberg, G. Winberg, C.-I. Branden, A. Kaske, I. Ernberg, and J. Coster Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier Genome Res., August 1, 2001; 11(8): 1404 - 1409. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Hess, J. Gasper, H. E. Hoekstra, C. E. Hill, and S. V. Edwards MHC Class II Pseudogene and Genomic Signature of a 32-kb Cosmid in the House Finch (Carpodacus mexicanus) Genome Res., May 1, 2000; 10(5): 613 - 623. [Abstract] [Full Text]
|
|