[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/.

[Interstitial telomere repeats as markers of evolutionary changes in the mammalian karyotype: human chromosome 2].

Telomer repeats represented by hexamer (TTAGGG)n at chromosome termini are required for correct function and chromosome stability. At the same time, interstitial telomer sequence (ITS) located far from the chromosome ends are known for several mammalian genomes, including the human genome. It is assumed that these repeats mark the points of fusion or other chromosome reconstructions of ancestors. Exact localization of all interstitial telomer sequences in the genome could greatly improve our understanding of the mechanism of karyotype evolution and species origin. We have developed a software for a search of interstitial telomer sequences in complete sequences of mammalian genomes. We have demonstrated the evolutionary significance of repeats by an example of human chromosome 2. The results and supplementary materials are available at the site of the Institute of Cytology and Genetics: http://www.bionet.nsc.ru/labs/theorylabmain/orlov/telomere/.

[Computer system "Gene Discovery" for searching for regularities in organization of eukaryotic regulatory sequences]. / Komp'iuternaia sistema "Gene Discovery" dlia poiska zakonomernostei organizatsii reguliatornykh posledovatel'nostei éukariot.

A method is proposed to automatically search for patterns in the mutual location of context signals in regulatory DNA sequences. The procedure is based on the methods of Data Mining and Knowledge Discovery software, implemented in a computer system Gene Discovery. This system was used to study erythroid-specific promoters and promoters of the endocrine-system genes from TRRD. We detected some trends in occurrence and localization of specific oligonucleotide groups.

[Precise recognition method of structure-function determinants of protein molecules]. / Metod tochnogo raspoznavaniia strukturno-funktsional'nykh determinant belkovykh molekul.

This paper is devoted to a computer system designed for formal description and knowledge about protein structural-functional determinants. Structural-functional determinant is a region of amino acid sequence with certain structural, functional or evolutionary properties specific for each class of macromolecules. Here the problem is solved by a special method which allows to design programs able to distinguish these structural-functional determinants. The method is based on the expert system technology and integrated data bases.