Quantification of DNA Patchiness Using Long-Range Correlation Measures
G. M. Viswanathan, S. V. Buldyrev, S. Havlin, and H. E. Stanley
Biophysical Journal, 72, 866-875 (Feb 1997)
Abstract
We introduce and develop new techniques to quantify DNA patchiness, and to
quantify characteristics of their mosaic structure. These techniques, which
involve calculating two functions, a(l) and b(l), measure correlations at
length scale l and detect distinct characteristic patch sizes embedded in
scale invariant patch size distributions. Using these new methods, we
address a number of issues relating to the mosaic structure of genomic
DNA. We find several distinct characteristic patch sizes in certain genomic
sequences, and compare, contrast, and quantify the correlation properties
of different sequences, including a number of yeast, human, and prokaryotic
sequences. We exclude the possibility that the correlation properties and
the known mosaic structure of DNA can be explained either by simple Markov
processes or by tandem repeats of dinucleotides. We find that the distinct
patch sizes in all sixteen yeast chromosomes are similar. Further, we test
the hypothesis that, for yeast, patchiness is caused by the alternation of
coding and noncoding regions, and also the hypothesis that in human sequences
patchiness is related to repetitive sequences. We find that, by themselves,
neither the alternation of coding and noncoding regions, nor repetitive
sequences, can fully explain the long-range correlation properties of DNA.
