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Mat. Biolog. Bioinform., 2009, Volume 4, Issue 2, Pages 66–80 (Mi mbb47)  

This article is cited in 1 scientific paper (total in 1 paper)

Bioinformatics

Phase shifts of the triplet periodicity in DNA sequences of genes

E. V. Korotkov, V. M. Rudenko

Centre "Bioengineering", Russian Academy of Sciences, Moscow, Russia

Abstract: Triplet periodicity is a well known property of the coding DNA sequences. But recently researches have shown that about 20% (122829) sequences from data bank KEGG (release 29) have not triplet periodicity without insertion/deletions on statistically significant level. The goal of this work was to show that the absence of triplet periodicity could be explained by shift of the open reading frame. To finding shifts of the open reading frame we suggest a new mathematical method based on calculation a measure of similarity between triplet periodicity types before and after the position of hypothetical open reading frame shift. Using developed method it was found 4724 sequences with possible open reading frame shifts. We assume that in these cases deletions and insertions were the cause of formation the new open reading frame and destruct the triplet periodicity. Revealed sequences were coded in amino acids sequences using current and ancient open reading frame. Ancient frames were obtained using shift information. 243 amino acids sequences, which were obtained by ancient reading frames, have similarities with proteins from Swiss-prot data bank. It confirms our assumption about possibility of genes evolution by open reading frame shifts.

Key words: DNA sequence, triplet periodicity, open reading frame, open reading frame shifts.

Full text: PDF file (576 kB)
References: PDF file   HTML file
UDC: 577.212.2+577.214
Received 04.08.2009, Published 07.09.2009

Citation: E. V. Korotkov, V. M. Rudenko, “Phase shifts of the triplet periodicity in DNA sequences of genes”, Mat. Biolog. Bioinform., 4:2 (2009), 66–80

Citation in format AMSBIB
\Bibitem{KorRud09}
\by E.~V.~Korotkov, V.~M.~Rudenko
\paper Phase shifts of the triplet periodicity in DNA sequences of genes
\jour Mat. Biolog. Bioinform.
\yr 2009
\vol 4
\issue 2
\pages 66--80
\mathnet{http://mi.mathnet.ru/mbb47}


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    Citing articles on Google Scholar: Russian citations, English citations
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    This publication is cited in the following articles:
    1. V. M. Rudenko, E. V. Korotkov, “Primenenie metoda Monte-Karlo dlya poiska potentsialnykh sdvigov ramki schityvaniya v genakh”, Matem. biologiya i bioinform., 6:1 (2011), 79–91  mathnet
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