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DNA Research Advance Access published online on March 3, 2009
DNA Research, doi:10.1093/dnares/dsp002
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© The Author 2009. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes

F.E. Frenkel and E.V. Korotkov

Bioengineering Centre of RAS, 60-letiya Oktyabrya prosp., 7/1, Moscow 117312, Russia

Received 26 August 2008 ; accepted 5 February 2009.

We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG's) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.

Key words: triplet periodicity; reading frame; shift

* To whom correspondence should be addressed. Tel. +7 499-135-2161. Fax. +7 499-135-0571. E-mail: felix.frenkel{at}gmail.com

Edited by Hiroyuki Toh


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