JZUS - Journal of Zhejiang University SCIENCE

Journal of Zhejiang University SCIENCE B 2005 Vol.6 No.8 P.743-755

http://doi.org/10.1631/jzus.2005.B0743

DNA sequence representation by trianders and determinative degree of nucleotides

Author(s): DUPLIJ Diana, DUPLIJ Steven
Affiliation(s): Institute of Molecular Biology and Genetics, Kiev 03143, Ukraine; more
Corresponding email(s): Steven.A.Duplij@univer.kharkov.ua
Key Words: DNA walk, Triander, Determinative degree, Analysis DNA sequences, Dystrophin, Nucleotide

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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 characteristic, the determinative degree, which reflects genetic code phenomenological properties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the “strength” of branch. A general method for identifying DNA sequence “by triander” which can be treated as a unique “genogram” (or “gene passport”) is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.

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