Bioinformatics, Vol 15, 644-653, Copyright © 1999 by Oxford University Press
VN Babenko, PS Kosarev, OV Vishnevsky, VG Levitsky, VV Basin and AS Frolov
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/.
ARTICLES
Investigating extended regulatory regions of genomic DNA sequences
Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru
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