Long-range correlations in DNA sequences using 2D DNA walk based on pairs of sequential nucleotides

Chaos, Solitons and Fractals

Volumn 22, Issue 4, 2004, Pages 947-955

  Zhang, Linxi ^a   Jiang, Zhouting ^a,b  

^a WENZHOU UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; ESCHERICHIA COLI; FOURIER TRANSFORMS; FUNCTIONS; GENES; LINEAR SYSTEMS; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; STATISTICAL METHODS;

AUTOCORRELATION FUNCTIONS; LOGARITHMIC PLOTS; NON-CODING SEQUENCES; NUCLEOTIDES;

DNA SEQUENCES;

EID: 2442468184     PISSN: 09600779     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chaos.2004.03.012     Document Type: Article

References (29)

1. Kolchanov N.A., Lim H.A. Computer analysis of genetic macromolecules: structure, function and evolution. 1994;World Scientific, Singapore.
2. Peng C.-K., Buldyrev S.V., Goldberger A.L., Havlin S., Sciortino F., Simons M., et al. Long-range correlation in nucleotide sequences. Nature (London). 356:1992;168-171.
3. α spectrum in a noncoding DNA sequence Europhys. Lett. 17:1992;655-660.
4. Voss R.F. Evolution of long-range fractal correlations and. 1/f noise in DNA base sequences Phys. Rev. Lett. 68:1992;3805-3808.
5. Mantegna R.N. Linguistic features of noncoding DNA sequences. Phys. Rev. Lett. 73:1994;3169-3172.
6. Israeloff N.E., Kagalenko M., Chan K. Can Zipf distinguish language from noise in noncoding DNA? Phys. Rev. Lett. 76:1996;1976.
7. Bonhoeffer S. No signs of hidden language in noncoding DNA. Phys. Rev. Lett. 76:1996;1977.
8. Voss R.F. Comment on "Linguistic features of noncoding DNA sequences" Phys. Rev. Lett. 76:1996;1978.
9. Herzel H., Grosse I. Correlations in DNA sequences: the role of protein segments. Phys. Rev. E. 55:1997;800-810.
10. Herzel H., Trifonov E.N., Weiss O., Grobe I. Interpreting correlations in biosequences. Physica A. 249:1998;449-459.
11. de Sousa Vieira M. Statistical of DNA sequences: a low-frequency analysis. Phys. Rev. E. 60:1999;5932-5937.
12. Li W. The study of correlation structures of DNA sequences: a critical review. Comput. Chem. 21:1997;257-271.
13. Buldyrev S.V., Goldberger A.L., Havlin S., Mantegna R.N., Matsa M.E., Peng C.-K., et al. Long-range correlation properties of coding and noncoding DNA sequences: genbank analysis. Phys. Rev. E. 51:1995;5084-5091.
14. Holste D., Weiss O., Grobe I., Herzel H. Are non-coding sequences of R. Prowazekii remants of 'neutralized' genes? J. Mol. Evol. 5:2000;335-362.
15. Bernaola-Galván P., Carpena P., Román-Roldán R., Oliver J.L. Study of statistical correlations in DNA sequences. Gene. 300:2002;105-115.
16. Peng C.-K., Buldyrev S.V., Goldberger A.L., Havlin S., Simons M., Stanley H.E. Finite-size effects on long-range correlations: Implications for analyzing DNA sequences. Phys. Rev. E. 47:1993;3730-3733.
17. Buldyrev S.V., Goldberger A.L., Havlin S., Peng C.-K., Simons M., Stanley H.E. Generalized Levy-walk model for DNA nucleotides. Phys. Rev. E. 47:1993;4514-4523.
18. Buldyrev S.V., Goldberger A.L., Havlin S., Peng C.-K., Stanley H.E., Stanley M.H.R., et al. Fractal landscapes and molecular evolution: modeling the myosin heavy chair gene family. Biophys. J. 65:1993;2673-2679.
19. Li W., Marr T.G., Kaneko K. Understanding long-range correlations in DNA sequences. Physica D. 75:1994;392-416.
20. Mantegna R.N., Buldyrev S.V., Goldberger A.L., Havlin S., Peng C.-K., Simons M., et al. Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics. Phys. Rev. E. 52:1995;2939-2950.
21. Berthelsen C.L., Glazier J.A., Skolnick M.H. Global fractal dimension of human DNA sequences treated as pseudorandom walks. Phys. Rev. A. 45:1992;8902-8913.
22. Hsu T.H., Nyeo S.L. Diffusion coefficients of two-dimensional viral DNA walks. Phys. Rev. E. 67:2003;051911-051918.
23. Tingting S., Linxi Z., Jin C., Zhouting J. Statistical properties and fractals of nucleotide clusters in DNA sequences. Chaos, Solitons & Fractals. 20:2004;1075-1084.
24. Jin C, Linxi Z, Delu Z. Long-range correlations in DNA sequences using two- and three-dimensional DNA walks. Chin J Polym Sci; in press.
25. Mandelbrot B.B. The fractal geometry of nature. 1982;Freeman, San Francisco.
26. Voss R.F. Random fractals: self-affinity in noise, music, mountains, and clouds. Physica D. 38:1989;362-371.
27. Feder J. Fractals. 1988;Plenum Press, New York.
28. Li W., Stolovitzky G., Bernaola-Galvan P., Oliver J.L. Compositional heterogeneity within and uniformity between DNA sequences of yeast chromosomes. Genome Res. 8:1998;916-928.
29. Yu Z.G., Anh V.V., Wang B. Correlation property of length sequences based on global structure of the complete genome. Phys. Rev. E. 63:2001;11903-11910.