Human-chimpanzee property-dependant comparisons on chromosomes 21

Motivation: Identification of different functional elements and their properties is a fundamental need in biomedical research, and phylogenctic comparisons form a solid basis for this task. But being applied to close genomes they can not "feel" such small, but nevertheless phenotypically important differences in sequence. Results: In this work we present the comparative analysis of two evolutionary close genomes - human and chimpanzee. In contrast to previous studies we focus on evolutionary differences and evaluate changes in DNA properties rather than count nucleotide mismatches. In our examples, we find that nucleotide mismatches in promoters were probably introduced in a correlated manner during the course of evolution. Such property-dependant conservation of promoters is significantly different from nucleotide conservation and shows significant functional biases.