Journal of Statistical Physics, Vol. 106, Nos. 1/2, January 2002. p. 23-56.
Clustering and long-range correlations in the nucleotide sequences of different categories of organisms are discussed. Clustering, mostly observed in higher eucaryotes, can be found at different length scales in DNA and Central Limit Theorems are used as links between these length scales. Several dynamical, statistical, mean-field models are proposed based on biologically motivated dynamical mechanisms and they successfully reproduce both the short range behavior observed in coding DNA and the long range, out-of-equilibrium features of non-coding DNA. Such dynamical mechanisms include aggregation of oligonucleotides, influx and DNA length reduction schemes, transpositions, and fusions of large DNA macromolecules. Fractality can be inferred from the short and long range correlations observed in the sequence structure of higher eucaryotes, where the non-coding part is relatively extended. In these organisms the DNA coding/non-coding alternation has the characteristics of finite size, fractal, random sets.