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


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

DUPLIJ Diana, DUPLIJ Steven. DNA sequence representation by trianders and determinative degree of nucleotides[J]. Journal of Zhejiang University Science B, 2005, 6(8): 743-755.

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publisher="Zhejiang University Press & Springer",

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T1 - DNA sequence representation by trianders and determinative degree of nucleotides
A1 - DUPLIJ Diana
A1 - DUPLIJ Steven
J0 - Journal of Zhejiang University Science B
VL - 6
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SP - 743
EP - 755
%@ 1673-1581
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.2005.B0743

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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


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