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

Molecular Biology and Evolution

Volumn 16, Issue 10, 1999, Pages 1391-1399

  Deschavanne, Patrick J ^a,b   Giron, Alain ^b   Vilain, Joseph ^b   Fagot, Guillaume ^b   Fertit, Bernard ^b  

^a INSTITUT JACQUES MONOD   (France)

^b INSERM   (France)

Author keywords

Characterization of species; Frequencies of oligonucleotides; Genomic signature; Image; Structure of genome

Indexed keywords

DNA;

ARTICLE; BACTERIAL GENETICS; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; GENE FREQUENCY; GENETIC ANALYSIS; GENOME; HUMAN; NONHUMAN;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0032823783     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026048     Document Type: Article

References (31)

1. BEUTLER, E., T. GELBART, J. HAN, J. A. KOZIOL, and B. BEUTLER. 1989. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc. Natl. Acad. Sci. USA 86:192-196.
2. BHAGWAT, A. S., and M. MCCLELLAND. 1992. DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res. 20:1663-1668.
3. BLAISDELL, B. E., K. E. RUDD, A. MATIN, and S. KARLIN. 1993. Significant dispersed recurrent DNA sequences in the Escherichia coli genome. J. Mol. Biol. 229:833-848.
4. BURGE, C., A. M. CAMPBELL, and S. KARLIN. 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA 89:1358-1362.
5. BURMA, P. K., A. RAJ, J. K. DEB, and S. K. BRAHMACHARI. 1992. Genome analysis: a new approach for visualization of sequence organization in genomes. J. Biosci. 17:395-411.
6. CHARLESWORTH, B. 1994. Patterns in the genome. Curr. Biol. 4:182-184.
7. DESCHAVANNE, P., and M. RADMAN. 1991. Counterselection of GATC sequences in enterobacteriophages by the components of the methyl-directed mismatch repair system J. Mol. Evol. 33:125-132.
8. DOOLITTLE, R. F. 1997. Microbial genomes opened up. Nature 392:339-342.
9. DUTTA, C., and J. DAS. 1992. Mathematical characterization of chaos game representation. New algorithms for nucleotide sequence analysis. J. Mol. Biol. 228:715-719.
10. FORSDYKE, D. R. 1995. Relative roles of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J. Mol. Evol. 41:573-581.
11. _. 1996. Different biological species "broadcast" their DNAs at different (G+C) "wavelengths." J. Theor. Biol. 178:405-417.
12. GELFAND, M. S., and E. V. KOONIN. 1997. Avoidance of palindromic words in bacterial and archeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 25: 2430-2439.
13. GOLDMAN, N. 1993. Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences. Nucleic Acids Res. 21: 2487-2491.
14. GUPTA, R. S. 1998a. Life's third domain (Archaea): an established fact or an endangered paradigm? Theor. Popul. Biol. 54:91-104.
15. _. 1998b. What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol. Microbiol. 29:695-707.
16. HILL, K. A., N. J. SCHISLER, and S. M. SINGH. 1992. Chaos game representation of coding regions of human globin genes and alcohol dehydrogenase genes of phylogenetically divergent species. J. Mol. Evol. 35:261-269.
17. JEFFREY, H. J. 1990. Chaos game representation of gene structure. Nucleic Acids Res. 18:2163-2170.
18. _. 1992. Chaos game visualization of sequences. Comput. Graphics 16:25-33.
19. JOSSE, J., A. D. KAISER, and A. KORNBERG. 1961. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxiribonucleic acid. J. Biol. Chem. 236:874-875.
20. KARLIN, S., and C. BURGE. 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11: 283-290.
21. KARLIN, S., C. BURGE, and A. M. CAMPBELL. 1992. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res. 20:1363-1370.
22. KARLIN, S., and I. LADUNGA. 1994. Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. USA 91:12832-12836.
23. KARLIN, S., J. MRÀZEK, and A. M. CAMPBELL. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179:3899-3913.
24. KENDALL, M. 1975. Multivariate analysis. Griffin, London.
25. MALEY, L. E., and C. R. MARSHALL. 1998. The coming of age of molecular systematics. Science 279:505-506.
26. MUTO, A., and S. OSAWA. 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84:166-169.
27. OLIVER, J. L., P. BERNAOLA-GALVÀN, G. GUERRERO, and R. ROMÀN-ROLDÀN. 1993. Entropic profiles of DNA sequences through chaos-game-derived images. J. Theor. Biol. 160: 457-470.
28. PHILLIPS, G. J., J. ARNOLD, and R. IVARIE. 1987. Mono-through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis. Nucleic Acids Res. 15: 2611-2626.
29. ROBINSON, N. J., P. J. ROBINSON, A. GUPTA, A. J. BLEASBY, B. A. WHITTON, and A. P. MORBY. 1995. Singular overrepresentation of an octameric palindrome, HIP1, in DNA from many cyanobacteria. Nucleic Acids Res. 23:729-735.
30. SHARP, P. M., and G. MATASSI. 1994. Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4:851-860.
31. WOESE, C. R., O. KANDLER, and M. L. WHEELIS. 1990. Towards a natural system of organisms: proposal for the domains archea, bacteria and eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.