CLC number: Q615
On-line Access: 2024-08-27
Received: 2023-10-17
Revision Accepted: 2024-05-08
Crosschecked: 0000-00-00
Cited: 1
Clicked: 6394
CHENG Jun, ZHANG Lin-xi. Statistical properties of nucleotide clusters in DNA sequences[J]. Journal of Zhejiang University Science B, 2005, 6(5): 408-412.
@article{title="Statistical properties of nucleotide clusters in DNA sequences",
author="CHENG Jun, ZHANG Lin-xi",
journal="Journal of Zhejiang University Science B",
volume="6",
number="5",
pages="408-412",
year="2005",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2005.B0408"
}
%0 Journal Article
%T Statistical properties of nucleotide clusters in DNA sequences
%A CHENG Jun
%A ZHANG Lin-xi
%J Journal of Zhejiang University SCIENCE B
%V 6
%N 5
%P 408-412
%@ 1673-1581
%D 2005
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2005.B0408
TY - JOUR
T1 - Statistical properties of nucleotide clusters in DNA sequences
A1 - CHENG Jun
A1 - ZHANG Lin-xi
J0 - Journal of Zhejiang University Science B
VL - 6
IS - 5
SP - 408
EP - 412
%@ 1673-1581
Y1 - 2005
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2005.B0408
Abstract: Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S)∝e−αs; values of the scaling exponent αCG are much larger than αAT; and αAT of 14 chromosomes are hardly changed, whereas αCG of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function ξ(m) of cluster C-G content showed that follows good power law ξ(m)∝m−γ. The average γ̄ for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of DNA sequences, and help us understand other properties of DNA sequences.
[1] Albert, B., Bray, D., Lewis, J., Raff, M., Robert, K., Watson, J.D., 1994. Molecular Biology of the Cell. Garland Publishing, New York.
[2] Azbel, M., 1973. Random two-component one-dimensional ising model for heteropolymer melting. Physical Review Letter, 31:589-593.
[3] Azbel, M., 1995. Universality in a DNA statistical structure. Physical Review Letters, 75:168-171.
[4] Azbel, M., Kantor, Y., Verkh, L., Vilenkin, A., 1982. Statistical analysis of DNA sequences. Biopolymers, 21:1687-1690.
[5] Buldyrev, S.V., Goldberger, A.L., Havlin, S., Mantegna, R.N., Matsa, M.E., Peng, C.K., Simons, M., Stanley, H.E., 1995. Long-range correlation properties of coding and noncoding DNA Sequences: GenBank analysis. Physical Review E, 51:5084-5091.
[6] Chen, J., Zhang, L.X., 2005. Scaling behaviors of DNA cluster for conding and non-conding sequence. Chaos Solitons & Fractals, 24:115-121.
[7] Cheng, J., Zhang, L.X., 2005. Scaling behaviours of C-G cluster for Chromosomes. Chaos Solitons & Fractals, 25:339-346.
[8] De Sousa Vieira, M., 1999. Statistics of DNA sequences: A low-frequency analysis. Physical Review E, 60:5932-5937.
[9] Herzel, H., Grobe, I., 1997. Correlations in DNA sequences: the role of protein coding segments. Physical Review E, 55:800-810.
[10] Herzel, H., Trifonov, E.N., Weiss, O., Grobe, I., 1998. Interpreting correlations in biosequences. Physica A, 248:449-459.
[11] Li, W., 1992. Generating nontrivial long-range correlations and 1/f spectra by replication and mutation. Int J Bif & Chaos, 2:137-154.
[12] Li, W., 1997. The study of correlation strctures of DNA sequences: a critical review. Journal of Computer Chemistry, 21:257-271.
[13] Li, W., Kaneko, K., 1992. Long-range correlation and partial 1/f α spectrum in a noncoding DNA squence. Europhysics Letter, 17:655-660.
[14] Peng, C.K., Buldyrev, S.V., Havlin, S., Simonis, M., Stanley, H.E., Goldberger, A.L., 1994. Mosaic organization of DNA nucleotides. Physical Review E, 49:1685-1689.
[15] Poland, D., 2004. The persistence exponent of DNA. Biophysical Chemistry, 110:59-72.
[16] Provata, A., Almirantis, Y., 1997. Mosaic organization of DNA sequences. Physica A, 247:482-487.
[17] Provata, A., Almirantis, Y., 2002. Statistical dynamics of DNA clustering. Journal Statistial Physics, 106:23-56.
[18] Sun, T.T., Zhang, L.X., Chen, J., Jiang, Z.T., 2004. Statistical properties and fractals of nucleotide clusters in DNA sequences. Chaos Solitons & Fractals, 20:1075-1084.
[19] Viswanathan, G.M., Buldyrev, S.V., Havlin, S., Stanley, H.E., 1998. Long-rang correlation measures for quantifying patchiness: Deviations from uniform power-law scaling in genomic DNA. Physica A, 249:581-586.
[20] Voss, R.F., 1992. Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Physical Review Letters, 68:3805-3808.
Open peer comments: Debate/Discuss/Question/Opinion
<1>