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Abstract
Computer prediction of nucleosome positioning sites from DNA sequences is of great impor- tance for analyzing eukaryotic gene expression regulation. Investigation of experimentally found nucleosome positioning sites determined statistically significant contexts and revealed symmetry of their distribution about the center of a site. Internet-available software was developed to determine the profile of preference of genomic DNA for nucleosome formation (nucleosome potential) on the basis of Markov mod- els. A correlation of the nucleosome potential with the complexity of the nucleotide sequence text was es- tablished. The nucleosome potential was estimated for transcription factor binding sites, promoters, exons, and introns of eukaryotic genes. A difference in nucleosome potential between promoters of tissue-specific and constitutively expressed eukaryotic genes was shown. The software is available at the website of the In- stitute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences at the address http://wwwmgs.bionet.nsc.ru/programs/VMM/.
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