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Classification of triplet periodicity in the DNA sequences of genes from KEGG databank

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Abstract

Totally, 472 288 regions of triplet periodicity were found in 578 868 genes from KEGG databank version 29 and classified. A new concept of triplet periodicity class and a measure of similarity between periodicity classes were introduced. Overall, 2520 classes were created and contained 94% of the triplet periodicity cases found. A similar correlation between the triplet periodicity and reading frame was observed for 92% of triplet periodicity regions contained in different classes. The remaining triplet periodicity regions displayed a shift of the reading frame relative to that common for the majority of genes belonging to the same triplet periodicity class. The hypothetical amino acid sequences were deduced from the periodicity regions according to the reading frame characteristic of the given triplet periodicity class. BLAST analysis demonstrated that 2660 hypothetical amino acid sequences display a statistically significant similarity to proteins from the Uni-Prot databank. It was supposed that 8% of the triplet periodicity regions contained in the classes have frameshift mutations. The triplet periodicity classes can be used to identify the coding regions in genes and to searching for frameshift mutations.

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

    F. E. Frenkel & E. V. Korotkov

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  1. F. E. Frenkel
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  2. E. V. Korotkov
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Correspondence to F. E. Frenkel.

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Original Russian Text © F.E. Frenkel, E.V. Korotkov, 2008, published in Molekulyarnaya Biologiya, 2008, Vol. 42, No. 4, pp. 707–720.

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Frenkel, F.E., Korotkov, E.V. Classification of triplet periodicity in the DNA sequences of genes from KEGG databank. Mol Biol 42, 629–640 (2008). https://doi.org/10.1134/S0026893308040201

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