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Volume 4   Issue 2   Year 2009
Phase Shifts of the Triplet Periodicity in DNA Sequences of Genes

Korotkov E.V. , Rudenko V.M.

Bioengineering Center of Russian Academy of Sciences, Moscow, 117312, 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.


Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2009.4.66
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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