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.