Full Text:
<2898>
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: 6067
Scaling behavior of nucleotide cluster in DNA sequences
| |||||||||||||
CHENG Jun, TONG Zi-shuang, ZHANG Lin-xi. Scaling behavior of nucleotide cluster in DNA sequences[J]. Journal of Zhejiang University Science B, 2007, 8(5): 359-364.
@article{title="Scaling behavior of nucleotide cluster in DNA sequences",
author="CHENG Jun, TONG Zi-shuang, ZHANG Lin-xi",
journal="Journal of Zhejiang University Science B",
volume="8",
number="5",
pages="359-364",
year="2007",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2007.B0359"
}
%0 Journal Article
%T Scaling behavior of nucleotide cluster in DNA sequences
%A CHENG Jun
%A TONG Zi-shuang
%A ZHANG Lin-xi
%J Journal of Zhejiang University SCIENCE B
%V 8
%N 5
%P 359-364
%@ 1673-1581
%D 2007
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2007.B0359
TY - JOUR
T1 - Scaling behavior of nucleotide cluster in DNA sequences
A1 - CHENG Jun
A1 - TONG Zi-shuang
A1 - ZHANG Lin-xi
J0 - Journal of Zhejiang University Science B
VL - 8
IS - 5
SP - 359
EP - 364
%@ 1673-1581
Y1 - 2007
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2007.B0359
Abstract: In this paper we study the scaling behavior of nucleotide cluster in 11 chromosomes of Encephalitozoon cuniculi Genome. The statistical distribution of nucleotide clusters for 11 chromosomes is characterized by the scaling behavior of P(S)∝e-αS, where S represents nucleotide cluster size. The cluster-size distribution P(S1+S2) with the total size of sequential C-G cluster and A-T cluster S1+S2 were also studied. P(S1+S2) follows exponential decay. There does not exist the case of large C-G cluster following large A-T cluster or large A-T cluster following large C-G cluster. We also discuss the relatively random walk length function L(n) and the local compositional complexity of nucleotide sequences based on a new model. These investigations may provide some insight into nucleotide cluster of DNA sequence.
[1] Arnéodo, A., 1998. Nucleotide composition effects on the long-range correlation in human genes. Eur. Phys. J. B, 1(2):259-263.
[2] Azbel, M., 1973. Random two-component one-dimensional Ising model for heteropolymer melting. Phys. Rev. Lett., 31(9):589-593.
[3] Azbel, M.Y., Kantor, Y., Verkh, L., Vilenkin, A., 1982. Statistical analysis of DNA sequences. Biopolymers, 21(8):1687-1690.
[4] Chen, J., Zhang, L.X., Cheng, J., 2004. Elastic behavior of adsorbed polymer chains. J. Chem. Phys., 121(22):11481-11488.
[5] Cheng, J., Zhang, L.X., 2005a. Scaling behaviors of CG clusters for chromosomes. Chaos, Solitons & Fractals, 25(2):339-346.
[6] Cheng, J., Zhang, L.X., 2005b. Statistical properties of nucleotide clusters in DNA sequences. Journal of Zhejiang University SCIENCE, 6B(5):408-412.
[7] Feder, J., 1989. Fractals. Plenum Press, New York.
[8] Gromiha, M.M., 2005. Influence of DNA stiffness in protein-DNA recognition. J. Biotechnology, 117(2):137-145.
[9] Gromiha, M.M., Munteanu, M.G., Simon, I., Pongor, S., 1997. The role of DNA bending in Cro protein-DNA interactions. Biophys. Chem., 69(2-3):153-160.
[10] Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A., 2004. Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J. Mol. Biol., 337(2):285-294.
[11] Harrington, R.E., Winicov, I., 1994. New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. Prog. Nucleic. Acid. Res. Mol. Biol., 47:195-270.
[12] Hogan, M.E., Austin, R.H., 1987. Importance of DNA stiffness in protein-DNA binding specificity. Nature, 329(6136):263-266.
[13] Mandelbrot, B.B., 1982. The Fractal Geometry of Nature. W.H. Freeman and Company, New York.
[14] Olson, W.K., Swigon, D., Coleman, B.D., 2004. Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, 362(1820):1403-1422.
[15] Poland, D., 2004. The persistence exponent of DNA. Biophys. Chem., 110(1-2):59-72.
[16] Provata, A., Almirantis, Y., 1997. Scaling properties of coding and noncoding DNA sequences. Physica A Statistical and Theoretical Physics, 247(1-4):482-487.
[17] Provata, A., Almirantis, Y., 2002. Statistical dynamics of DNA clustering in the genome structure. J. Stat. Phys., 106(1/2):23-56.
[18] Salamon, P., Konopka, A.K., 1992. A maximum entropy principle for the distribution of local complexity in naturally occurring nucleotide sequences. Comput. Chem., 16(2):117-124.
[19] Salamon, P., Wooten, J.C., Konopka, A.K., Hansen, L.K., 1993. On the robustness of maximum entropy relationships for complexity distributions of nucleotide sequences. Comput. Chem., 17(2):135-148.
[20] Sugiarto, R., Han, L.Y., Wang, J.S., Chen, Y.Z., 2006. Super paramagnetic clustering of DNA sequences. J. Biol. Phys., 32(1):11-25.
[21] 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(5):1075-1084.
[22] Vaillant, C., Audit, B., Thermes, C., Arnéodo, A., 2003. Influence of the sequence on elastic properties of long DNA chains. Phys. Rev. E, 67(3):032901-032904.
[23] Wootton, J.C., Federhen, S., 1993. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17(2):149-163.
[24] Zhang, L.X., Jiang, Z.T., 2004. Long-range correlations in DNA sequences using 2D DNA walk based on pairs of sequential nucleotides. Chaos, Solitons & Fractals, 22(4):947-955.
[25] Zhang, L.X., Chen, J., 2005. Scaling behaviors of CG cluster for coding and non-coding DNA sequence. Chaos, Solitons & Fractals, 24(1):115-123.
Open peer comments: Debate/Discuss/Question/Opinion
<1>