Determinative degree and nucleotide sequence analysis by trianders

Abstract

A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristics, the determinative degree, which reflects phenomenological properties of genetic code and is adjusted to nucleotides physical properties. We consider each position in codon independently, which gives three separate walks being characterized by different angles and lengths, and such an object is called triander which reflects the "strength" of branch. A general method of identification of DNA sequence "by triander", which can be treated as a unique "genogram", "gene passport" is proposed. The two- and three-dimensional trianders are considered. The difference of sequence fine structure in genes and the intergenic space is shown. A clear triplet signal in coding locuses is found which is absent in the intergenic space and is independent from the sequence length. The topological classification of trianders is presented which can allow us to provide a detail working out signatures of functionally different genomic regions.