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In the present paper the dynamics of the nonlinear conformational excitations--kinks, in inhomogeneous polynucleotide DNA chains is investigated. To calculate the kink rest energy E0 and its length d the method of dynamical interval is used. This makes it possible to take into account that all coefficients of the model dynamic equation--the sine-Gordon equation depend on the sequence of bases. It is shown that the method gives an opportunity to calculate dynamical characteristics of any artificial and real sequences that is important for implementing tasks associated with the search and analysis of functionally important DNA sites.

Identification of groups of co-regulated genes (regulons) is an important part of studying transcriptional regulation. One possible approach is to cluster regulatory sites that were found using experimental or computational techniques, such as phylogenetic footprinting. This strategy doesn't require a priori knowledge about co-regulation and allows finding putative new members of known groups of co-regulated genes (i.e. a new regulon). Also, it allows finding new putative regulons, which is especially important for poorly annotated genomes. We have developed ClusterTree-RS, an algorithm for clustering regulatory signals using binary trees; it is presented in this paper along with some testing results on simulated and real data. The algorithm is implemented in Java and took about 2 hours 40 minutes to cluster 1500 input signals on a computer with AMD Athlon 1.91 GHz CPU.