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Identification of different functional elements and their properties is a fundamental need in biomedical research and phylogenetic comparisons of a growing number of sequenced genomes form a solid basis for this task. Most available phylogenetic approaches are focused on searching for individual sequence alterations, responsible for the observed phenotype, or statistically evaluate observed mutations to infer general trends. However, being applied to close genomes such methods suffer from poor statistics of rare mutations and give only (at its best) coarse results concerning the potential functional importance of the nucleotide differences. However, quantifying the changes in physical properties of DNA allows to see the strength of introduced mutations and hence to classify them for further investigations. In this work we present the comparative sequence analysis of two evolutionarily close species-human and chimpanzee. In contrast to previous studies we evaluate changes in melting enthalpy of DNA rather than count nucleotide mismatches. We find that nucleotide mismatches in promoters were apparently introduced in a correlated manner during the course of evolution, so that, for example, the DNA property "melting enthalpy" was retained. Such property conservation of promoters is significantly different from nucleotide conservation, shows significant positional and functional biases, and seems to represent a novel feature of gene regulation.

FeatureScan is a software package aiming to reveal novel types of DNA sequence similarity by comparing physico-chemical properties. Thirty-eight different parameters of DNA double strands such as charge, melting enthalpy, conformational parameters and the like are provided. As input FeatureScan requires two sequences, a pattern sequence and a target sequence, search conditions are set by selecting a specific DNA parameter and a threshold value. Search results are displayed in FASTA format and directly linked to external genome databases/browsers (ENSEMBL, NCBI, UCSC). An Internet version of FeatureScan is accessible at http://genome.gbf.de/featurescan/. As part of the HOBIT initiative (http://hobit.sourceforge.net/) FeatureScan is also accessible as a web service at its above home page. Currently, several preloaded genomes are provided at this Internet website (Homo sapiens, Mus musculus, Rattus norvegicus and four strains of Escherichia coli) as target sequences. Standalone executables of FeatureScan are available on request.