Journal Article

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

F.E. Frenkel and E.V. Korotkov

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 16, issue 2, pages 105-114
Published in print April 2009 | ISSN: 1340-2838
Published online March 2009 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsp002

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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.

Keywords: triplet periodicity; reading frame; shift

Journal Article.  6729 words.  Illustrated.

Subjects: Genetics and Genomics

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