Document Detail


DNA sequence representation by trianders and determinative degree of nucleotides.
MedLine Citation:
PMID:  16052707     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Diana Duplij; Steven Duplij
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Publication Detail:
Type:  Evaluation Studies; Journal Article    
Journal Detail:
Title:  Journal of Zhejiang University. Science. B     Volume:  6     ISSN:  1673-1581     ISO Abbreviation:  J Zhejiang Univ Sci B     Publication Date:  2005 Aug 
Date Detail:
Created Date:  2005-07-29     Completed Date:  2005-12-01     Revised Date:  2013-06-09    
Medline Journal Info:
Nlm Unique ID:  101236535     Medline TA:  J Zhejiang Univ Sci B     Country:  China    
Other Details:
Languages:  eng     Pagination:  743-55     Citation Subset:  IM    
Affiliation:
Institute of Molecular Biology and Genetics, Kiev 03143, Ukraine.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Base Sequence
Chromosome Mapping / methods*
Codon / genetics*
DNA / genetics*
Molecular Sequence Data
Nucleotides / genetics*
Sequence Analysis, DNA / methods*
Chemical
Reg. No./Substance:
0/Codon; 0/Nucleotides; 9007-49-2/DNA
Comments/Corrections

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