Biomedical subjects

V G Levitsky

Publications and source records attributed to V G Levitsky.

4 recordsLinked to original sources

PubMed2001

Nucleosome formation potential of exons, introns, and Alu repeats.

A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites.

Alu Elements↗

PubMed2001

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.

MOTIVATION: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation. RESULTS: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression. AVAILABILITY: The program for nucleosome sites recognition is included into the GeneExpress system; section 'DNA Nucleosomal Organization', http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/.

Algorithms↗

PubMedDate not supplied

Nucleosomal DNA property database.

MOTIVATION: Chromatin structure plays the crucial role in proper gene functioning. Therefore, it is very important to investigate nucleosomal DNA properties and recognize genome nucleosome positioning sequences. Nevertheless, applying different sequence analysis methods separately is insufficient for complete nucleosomal DNA description. One of the most probable reasons for that is the weakness of nucleosome positioning signals. The present paper offers a set of methods to reveal the most important nucleosomal DNA characteristics and to show a common pattern of nucleosome site properties. RESULTS: A complex approach was used to determine conformational and physicochemical properties that are most significant for nucleosome binding site description. The integrated database of nucleosomal DNA properties is compiled. This database comprises different sections for description of DNA characteristics. Revealing significant DNA characteristics allows the classification of various samples of site sequences and the generation of programs for site recognition. AVAILABILITY: The current version of the database is available at http://wwwmgs.bionet.nsc. ru/system/BDNAvideo/. C-code of the recognition program may be found in the section FEATURE. WWW-available programs for testing arbitrary sequences are accessible at http://wwwmgs.bionet.nsc. ru/Programs/bDNA/NA_bDNA.htm/. The links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

Algorithms↗

PubMedDate not supplied

Investigating extended regulatory regions of genomic DNA sequences.

MOTIVATION: Despite the growing volume of data on primary nucleotide sequences, the regulatory regions remain a major puzzle with regard to their function. Numerous recognising programs considering a diversity of properties of regulatory regions have been developed. The system proposed here allows the specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions. RESULTS: The Internet-accessible computer system RegScan, designed to analyse the extended regulatory regions of eukaryotic genes, has been developed. The computer system comprises the following software: (i) programs for classification dividing a set of promoters into TATA-containing and TATA-less promoters and promoters with and without CpG islands; (ii) programs for constructing (a) nucleotide frequency profiles, (b) sequence complexity profiles and (c) profiles of conformational and physico-chemical properties; (iii) the program for constructing the sets of degenerate oligonucleotide motifs of a specified length; and (iv) the program searching for and visualising repeats in nucleotide sequences. The system has allowed us to demonstrate the following characteristic patterns of vertebrate promoter regions: the TATA box region is flanked by regions with an increased G+C content and increased bending stiffness, the TATA box content is asymmetric and promoter regions are saturated with both direct and inverted repeats. AVAILABILITY: The computer system RegScan is available via the Internet at http://www.mgs.bionet.nsc. ru/Systems/RegScan, http://www.cbil.upenn.edu/mgs/systems/r egscan/.

Algorithms↗