TY - JOUR
T1 - Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences
AU - Buldyrev, Sergey V.
AU - Dokholyan, Nikolay V.
AU - Havlin, Shlomo
AU - Stanley, H. Eugene
AU - Stanley, Rachel H.R.
N1 - Funding Information:
We would like to thank N. Broude, C. Cantor, R.S. Dokholyan, M. Frank-Kamenetskii, A. Goldberger, M. Goodman, A.Yu. Grosberg, I. Grosse, I Labat, R.N. Mantegna, C.-K. Peng, E.I. Shakhmonvich, A. Shehter, M. Simons, C. Smith, F. Starr, E.N. Trifonov, G.M. Viswanathan, G.H. Weiss, and R. Wells for fruitful discussions. This work is supported by NIH-HGP. N.V.D. is supported by NIH NRSA molecular biophysics predoctoral traineeship (GM08291-09).
PY - 1999/11/1
Y1 - 1999/11/1
N2 - 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.
AB - 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.
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U2 - 10.1016/S0378-4371(99)00338-6
DO - 10.1016/S0378-4371(99)00338-6
M3 - Conference article
AN - SCOPUS:0347661852
SN - 0378-4371
VL - 273
SP - 19
EP - 32
JO - Physica A: Statistical Mechanics and its Applications
JF - Physica A: Statistical Mechanics and its Applications
IS - 1-2
T2 - Proceedings of the 1999 13th Max Born Symposium on 'Statistical Physics in Biology: Perspectives in DNA Analysis, Population Dynamics and Ageing'
Y2 - 26 May 1999 through 30 May 1999
ER -