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 Mat. Biolog. Bioinform., 2012, Volume 7, Issue 2, Pages 461–475 (Mi mbb116)

Bioinformatics

Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes

Valentina M. Pugacheva, Alexander E. Korotkov, Eugene V. Korotkov

Bioengineering Centre of RAS, Russian Academy of Sciences, Moscow 117312, Russia

Abstract: This paper presents developed mathematical method for searching pair phase shifts of triplet periodicity. Such phase shifts could be a potential frameshifts in genes resulting the insertions of quite long DNA fragments. We developed software and checked if there are pair phase shifts of triplet periodicity in genes of 17 bacteria genomes. The results shows that there is about 1 percent of bacteria genes having pair phase shift of triplet periodicity in these 17 genoms. This paper also describes developed method for visualization of pair phase shifts of triplet periodicity and gives an examples of such shifts. Research results were partially confirmed by the search for aminoacids sequences similarities that had been made by alternative reading frames. The connection between pair phase shifts of triplet periodicity and frameshift in genes is disscussed.

Key words: triplet periodicity, reading frame, frameshifts, phase.

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UDC: 577.212.2

Citation: Valentina M. Pugacheva, Alexander E. Korotkov, Eugene V. Korotkov, “Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes”, Mat. Biolog. Bioinform., 7:2 (2012), 461–475

Citation in format AMSBIB
\Bibitem{PugKorKor12} \by Valentina~M.~Pugacheva, Alexander~E.~Korotkov, Eugene~V.~Korotkov \paper Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes \jour Mat. Biolog. Bioinform. \yr 2012 \vol 7 \issue 2 \pages 461--475 \mathnet{http://mi.mathnet.ru/mbb116}