[Statistical analysis of nucleosome formation sites]

The prediction of the DNA capacity to form nucleosome structure based on sequence statistics is of importance in the analysis of gene expression regulation in eukaryotes. A context analysis of nucleotide sequences of experimentally defined sites of nucleosome formation made it possible to determine the sequence preference for nucleosome formation on the basis of statistical information. An improved version of the Markov model was developed to predict the preference of DNA sequences to be within a nucleosome structure. The developed VMM (Variable Memory Markov model) program computes the nucleosome formation potential for genomic DNA sequences of arbitrary lengths, including the short transcription factor binding sites. Differences in nucleosome potential for exons, introns, and promoters were revealed. A correlation of the nucleosome potential estimate with text complexity was established. The VMM is available at http://wwwmgs. bionet.nsc.ru/programs/VMM/.