Affiliations: Department of Genome Analysis, GBF (German Research
Centre for Biotechnology), D-38124 Braunschweig, Germany | Institute of Cytology and Genetics SB RAS,
Novosibirsk, Russia | BIOBASE GmbH, D-38300 Wolfenbüttel, Germany | University of Applied Sciences, D-26723 Emden,
Abstract: We present an implementation of the signal theory-based approach for
detection of novel types of DNA similarity which are based on physical
properties of DNA. Systematic study of the sensitivity of the new similarity
measure revealed qualitative differences to letter-based similarity. A variety
of physical parameters of DNA double strands, which in a straightforward way
reflect different kinds of information hidden behind the primary structure of
DNA, showed a wide range of recognition power of the signal similarity measure.
We applied the novel DNA similarity measure for the analysis of promoters of E.
coli genes. We found that promoter similarities revealed by our approach
correlate with their transcription regulatory responsivenesses to different
antibiotic and osmotic treatments. Accelerated by special hardware for fast
Fourier transformations, the method is easily applicable for the analysis of
entire eukaryotic genomes in minutes.
Keywords: Signal theory, pattern recognition, promoter similarities, FeatureScan