Mutually symmetric and complementary triplets: Differences in their use distinguish systematically between coding and non-coding genomic sequences

Journal of Theoretical Biology

Volumn 223, Issue 4, 2003, Pages 477-487

  Nikolaou, Christoforos ^a   Almirantis, Yannis ^a  

^a INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

Author keywords

Codon asymmetries; Codon structure; DNA linguistics

Indexed keywords

GENETICS;

ALGORITHM; ARTICLE; CODON; CONTROLLED STUDY; EUKARYOTIC CELL; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENOME ANALYSIS; INTERMETHOD COMPARISON; INTRON; LINGUISTICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE; PRIORITY JOURNAL; SYMBIOSIS;

EID: 0038380649     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-5193(03)00123-1     Document Type: Article

References (63)

1. Almirantis Y. A standard deviation based quantification differentiates coding from non-coding DNA sequences and gives insight to their evolutionary history. J. theor. Biol. 196:1999;297-308.
2. Almirantis Y., Provata A. Long- and short-range correlations in genome organisation. J. Statist. Phys. 97:1999;233-262.
3. Almirantis Y., Provata A. An evolutionary model for the origin of non-randomness, long-range order and fractality in the genome. BioEssays. 23:2001;647-656.
4. Arneodo A., Bacry E., Graves P.V., Muzy J.F. Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett. 74:1995;3293-3296.
5. Arquès D.G., Michel C.J. A complementary circular code in the protein coding genes. J. theor. Biol. 182:1996;45-58.
6. Arquès D.G., Michel C.J. A circular code in the protein coding genes of mitochondria. J. theor. Biol. 189:1997;273-290.
7. Arquès D.G., Fallot J.P., Michel C.J. An evolutionary model of a complementary circular code. J. theor. Biol. 185:1997;241-253.
8. Arquès D.G., Fallot J.P., Michel C.J. An evolutionary analytical model of a complementary circular code simulating the protein coding genes, the 5′ and 3′ regions. Bull. Math. Biol. 60:1998;163-194.
9. Beckmann J.S., Brendel V., Trifonov E.N. Intervening sequences exhibit distinct vocabulary. J. Biomol. Struct. Dyn. 4:1986;391-399.
10. Bernaola-Galvan P., Grosse I., Carpena P., Oliver J.L., Roman-Roldan R., Stanley H.E. Finding borders between coding and noncoding DNA regions by an entropic segmentation method. Phys. Rev. Lett. 85:2000;1342-1345.
11. Blaisdell B.E. A measure of the similarity of sets of sequences not requiring sequence allignment. Proc. Natl Acad. Sci. USA. 83:1986;5155-5159.
12. Brendel V., Beckmann J.S., Trifonov E.N. Linguistics of nucleotide sequences. morphology and comparison of vocabularies J. Biomol. Struct. Dyn. 4:1986;11-21.
13. Buldyrev S.V., Goldberg A.L., Havlin S., Peng C.K., Simons M., Stanley H.E. Generalized Levy-walk model for DNA nucleotide sequences. Phys. Rev. E. 47:1993;4514-4523.
14. Burge C., Cambell A.M., Karlin S. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl Acad. Sci. USA. 89:1992;1358-1362.
15. Crick F.H.C., Brenner S., Klug A., Pieczenik G. A speculation on the origin of protein synthesis. Origins of life. 7:1976;389-397.
16. Ebeling W., Nicolis G. Word frequency and entropy of symbolic sequences. a dynamical perspective Chaos Solitons Fractals. 2:1992;635-650.
17. Eigen M., Schuster P. The Hypercycle. 1979;Springer, Berlin, Heidelberg, New York.
18. Faxen M., Plumbridge J., Isaksson L.A. Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glns. Nucl. Acid. Res. 19:1991;5247-5251.
19. Gutierrez G., Oliver J.L., Marin A. Dinucleotides and G+C content in human genes. opposite behavior of GpG, GpC and TpC at II-III coding positions and in introns J. Mol. Evol. 37:1993;131-136.
20. Hanai R., Wada A. Novel third-letter bias in Escherichia coli codons revealed by rigorous treatment of coding constraints. J. Mol. Biol. 207(4):1989;655-660.
21. Hao B.-L. Fractals from genomes. Modern Phys. Lett. 14:2000;871-875.
22. Herdan G. The Advanced Theory of Language as Choice and Chance. 1966;Springer, Berlin, Heidelberg, New York.
23. Herzel H., Ebeling W., Schmitt A.O. Entropies of biosequences. the role of repeats Phys. Rev. E. 50:1994;5061-5071.
24. Hoel P.G. Introduction to Methematical Statistics. 3rd Edition:1966;Wiley, New York.
25. Holmquist G.P. Evolution of chromosomal bands. molecular ecology of noncoding DNA J. Mol. Evol. 28:1989;469-486.
26. Hong J. Prediction of oligonucleotide frequencies based upon dinucleotide frequencies obtained from the nearest neighbor analysis. Nucl. Acid. Res. 18:1989;2625-2628.
27. Ikemura T., Wada K. Evident diversity of codon usage patterns in human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenic data. Nucl. Acid. Res. 19:1991;4333-4339.
28. Ioshikhes I., Bolshoy A., Derenshteyn K., Borodovsky M., Trifonov E.N. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262:1996;129-139.
29. Jimenez-Montano M.A., Ebeling W., Pohl T., Rapp P.E. Entropy and complexity of finite sequences as fluctuating quantities. Biosystems. 64:2002;23-32.
30. Josse J., Kaiser A.D., Kornberg A. Synthesis of deoxyribonucleic acid. VIII frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J. Biol. Chem. 236:1961;864-875.
31. Jungck J.R. The genetic code as a periodic table. J. Mol. Evol. 11:1978;211-224.
32. Karlin S., Burge C. Dinucleotide relative abundance extremes. a genomic signature TIG. 11:1995;283-290.
33. Karlin S., Ladunga I. Comparisons of eukaryotic genomic sequences. Proc. Natl Acad. Sci. USA. 91:1994;12832-12836.
34. Karlin S., Mrazek J. Compositional differences within and between eukaryotic genomes. Proc. Natl Acad. Sci. USA. 94:1997;10227-10232.
35. Karlin S., Burge C., Campbell A.M. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucl. Acid. Res. 20:1992;1363-1370.
36. Karlin S., Ladunga I., Blaisdell B.E. Heterogeneity of genomes. measures and values Proc. Natl Acad. Sci. USA. 91:1994;12837-12841.
37. Knuth D.E. The Art of Computer Programming. 1981;Addison-Westley, Reading, MA.
38. Kumar A., Bennetzen L. Plant retrotransposons. Ann. Rev. Genet. 33:1999;479-532.
39. Li W. The study of correlation structures of DNA sequences - a critical review. Comput. Chem. 21:1997;257-272.
40. Li W., Kaneko K. Long-range correlations and partial 1/fa spectrum in a noncoding DNA sequence. Europhys. Lett. 17:1992;655-660.
41. Mani G.S. Correlations between the coding and non-coding regions in DNA. J. theor. Biol. 158:1992;429-445.
42. Manning C.D., Schutze H. Foundations of Statistical Natural Languages Processing. 1999;The MIT press, Cambridge, MA.
43. Nakamura Y., Gojobori T., Ikemura T. Codon usage tabulated from international DNA sequence databases. status for the year 2000 Nucl. Acid. Res. 28:2000;292.
44. Nicolis J.S., Katsikas A.A. Chaotic dynamics of linguistic-like processes at the syntactic and semantic levels. in the pursuit of a multifractal attractor Custi J.L., Karlqvist A. Cooperation and Conflict in General Evolutionary Processes. 1994;Willey, New York.
45. Nikolaou C., Almirantis Y. A study of the middle-scale nucleotide clustering in DNA sequences of various origin and functionality, by means of a method based on a modified standard deviation. J. theor. Biol. 217(4):2002;479-492.
46. Nussinov R. Nearest neighbor nucleotide patterns. J. Biol. Chem. 256:1981;8458-8462.
47. Nussinov R. The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice. J. Mol. Evol. 17:1981;237-244.
48. Peng C.K., Buldyrev S.V., Goldberger A.L., Havlin S., Sciortino F., Simons M., Stanley H.E. Long-range correlations in nucleotide sequences. Nature. 356:1992;168-170.
49. Phillips G.J., Arnold J., Ivarie R. Mono- through hexanucleotide composition of the Escherocjia coli genome. markov chain analysis Nucl. Acid. Res. 15:1987;2611-2626.
50. Provata A., Almirantis Y. Scaling properties of coding and non-coding DNA sequences. Physica A. 247:1997;482-496.
51. Provata A., Almirantis Y. Fractal cantor patterns in the sequence structure of DNA. Fractals. 8:2000;15-27.
52. Russell G.J., Walker P.M., Elton R.A., Subak-Sharpe J.H. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J. Mol. Biol. 108:1976;1-23.
53. Schmidt T. LINEs, SINEs and repetitive DNA. non-LTR retro-transposons in plant genomes Plant Mol. Biol. 40:1999;903-910.
54. Shepherd J.C. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl Acad. Sci. USA. 78(3):1981;1596-1600.
55. Shepherd J.C. Ancient patterns in nucleic acids sequences. Methods Enzymol. 183:1990;180-192.
56. Stückle E.E., Emmrich C., Grob U., Nielsen P.J. Statistical analysis of nucleotide sequences. Nucl. Acids Res. 18(22):1990;6641-6647.
57. Swartz M.N., Trautner T.A., Kornberg A. Synthesis of deoxyribo-nucleic acid. XI further studies on frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J. Biol. Chem. 237:1962;1961-1967.
58. Taylor F.J., Coates D. The code within the codons. Biosystems. 22:1989;177-187.
59. Ticher A., Graur D. Nucleic acid composition, codon usage and the rate of synonymous substitution in protein-coding genes. J. Mol. Evol. 28:1989;286-298.
60. Trifonov E.N., Sussman J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl Acad. Sci. USA. 77:1980;3816-3820.
61. Tsonis A.A., Elsner J.B., Tsonis P.A. Periodicity in DNA coding sequences. Implications in gene evolution. J. theor. Biol. 151:1991;323-331.
62. Voss R.F. Evolution of long-range fractal correlations and 1/f noice in DNA base sequences. Phys. Rev. Lett. 68:1992;3805-3808.
63. Wong J.T.F., Cedergren R. Natural selection versus primitive gene structure as determinant of codon usage. Eur. J. Biochem. 159:1986;175-180.