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Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

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  • Buldyrev, Sergey V.
  • Dokholyan, Nikolay V.
  • Havlin, Shlomo
  • Stanley, H.Eugene
  • Stanley, Rachel H.R.

Abstract

We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

Suggested Citation

  • Buldyrev, Sergey V. & Dokholyan, Nikolay V. & Havlin, Shlomo & Stanley, H.Eugene & Stanley, Rachel H.R., 1999. "Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 273(1), pages 19-32.
    • Handle: RePEc:eee:phsmap:v:273:y:1999:i:1:p:19-32
    DOI: 10.1016/S0378-4371(99)00338-6
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    References listed on IDEAS

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    1. Dokholyan, Nikolay V. & Buldyrev, Sergey V. & Havlin, Shlomo & Stanley, H.Eugene, 1998. "Model of unequal chromosomal crossing over in DNA sequences11This work is supported by NIH-HGP," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 249(1), pages 594-599.
    2. Buldyrev, S.V. & Dokholyan, N.V. & Goldberger, A.L. & Havlin, S. & Peng, C.-K. & Stanley, H.E. & Viswanathan, G.M., 1998. "Analysis of DNA sequences using methods of statistical physics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 249(1), pages 430-438.
    3. Herzel, H & Trifonov, E.N & Weiss, O & Große, I, 1998. "Interpreting correlations in biosequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 249(1), pages 449-459.
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    Cited by:

    1. Zhang, Linxi & Sun, Tingting, 2005. "Statistical properties of nucleotides in human chromosomes 21 and 22," Chaos, Solitons & Fractals, Elsevier, vol. 23(3), pages 1077-1085.

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