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. 1993 May 25;21(10):2487–2491. doi: 10.1093/nar/21.10.2487

Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.

N Goldman 1
PMCID: PMC309551  PMID: 8506142

Abstract

The chaos game representation (CGR) is a scatter plot derived from a DNA sequence, with each point of the plot corresponding to one base of the sequence. If the DNA sequence were a random collection of bases, the CGR would be a uniformly filled square; conversely, any patterns visible in the CGR represent some pattern (information) in the DNA sequence. In this paper, patterns previously observed in a variety of DNA sequences are explained solely in terms of nucleotide, dinucleotide and trinucleotide frequencies.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Almagor H. A Markov analysis of DNA sequences. J Theor Biol. 1983 Oct 21;104(4):633–645. doi: 10.1016/0022-5193(83)90251-5. [DOI] [PubMed] [Google Scholar]
  2. Avery P. J. The analysis of intron data and their use in the detection of short signals. J Mol Evol. 1987;26(4):335–340. doi: 10.1007/BF02101152. [DOI] [PubMed] [Google Scholar]
  3. Bird A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980 Apr 11;8(7):1499–1504. doi: 10.1093/nar/8.7.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blaisdell B. E. Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding. J Mol Evol. 1984;21(3):278–288. doi: 10.1007/BF02102360. [DOI] [PubMed] [Google Scholar]
  5. Bulmer M. A statistical analysis of nucleotide sequences of introns and exons in human genes. Mol Biol Evol. 1987 Jul;4(4):395–405. doi: 10.1093/oxfordjournals.molbev.a040453. [DOI] [PubMed] [Google Scholar]
  6. Dutta C., Das J. Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis. J Mol Biol. 1992 Dec 5;228(3):715–719. doi: 10.1016/0022-2836(92)90857-g. [DOI] [PubMed] [Google Scholar]
  7. Grantham R., Gautier C., Gouy M., Mercier R., Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980 Jan 11;8(1):r49–r62. doi: 10.1093/nar/8.1.197-c. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hill K. A., Schisler N. J., Singh S. M. Chaos game representation of coding regions of human globin genes and alcohol dehydrogenase genes of phylogenetically divergent species. J Mol Evol. 1992 Sep;35(3):261–269. doi: 10.1007/BF00178602. [DOI] [PubMed] [Google Scholar]
  9. JOSSE J., KAISER A. D., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem. 1961 Mar;236:864–875. [PubMed] [Google Scholar]
  10. Jeffrey H. J. Chaos game representation of gene structure. Nucleic Acids Res. 1990 Apr 25;18(8):2163–2170. doi: 10.1093/nar/18.8.2163. [DOI] [PMC free article] [PubMed] [Google Scholar]

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