Classification analysis of a latent dinucleotide periodicity of plant genomes View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2008-01

AUTHORS

A. A. Shelenkov, K. G. Skryabin, E. V. Korotkov

ABSTRACT

The information decomposition (ID) method has been used for searching dinucleotide periodicities, including latent ones, in plant genomes. In nucleotide sequences of genomes of various plants from the Gen-Bank database, 14 766 sequences with a periodicity of two nucleotides have been found at a high level of statistical significance. Classification of the periodicity matrices of the detected DNA sequences has yielded 141 classes of dinucleotide periodicity. Since ID does not detect periodicities with nucleotide deletions or insertions, modified profile analysis (MPA) has been applied to the obtained classes to reveal DNA sequences with dinucleotide periodicities containing nucleotide deletions and insertions. Combined use of ID and MPA has permitted the detection of 80 396 DNA sequences with dinucleotide periodicities in the genomes of various plants. The biological role of dinucleotide periodicity in the detected sequences is discussed. More... »

PAGES

101-114

Journal

TITLE

Russian Journal of Genetics

ISSUE

1

VOLUME

44

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1134/s1022795408010134

DOI

http://dx.doi.org/10.1134/s1022795408010134

DIMENSIONS

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51 schema:description The information decomposition (ID) method has been used for searching dinucleotide periodicities, including latent ones, in plant genomes. In nucleotide sequences of genomes of various plants from the Gen-Bank database, 14 766 sequences with a periodicity of two nucleotides have been found at a high level of statistical significance. Classification of the periodicity matrices of the detected DNA sequences has yielded 141 classes of dinucleotide periodicity. Since ID does not detect periodicities with nucleotide deletions or insertions, modified profile analysis (MPA) has been applied to the obtained classes to reveal DNA sequences with dinucleotide periodicities containing nucleotide deletions and insertions. Combined use of ID and MPA has permitted the detection of 80 396 DNA sequences with dinucleotide periodicities in the genomes of various plants. The biological role of dinucleotide periodicity in the detected sequences is discussed.
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