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Bioinformatic analysis of inverted repeats of coronaviruses genome

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Author(s): Limanskaya O. Yu.

Journal: Biopolymers and Cell
ISSN 0233-7657

Volume: 25;
Issue: 4;
Start page: 307;
Date: 2009;
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Keywords: severe acute respiratory syndrome virus | coro- navirus | hairpin structure | inverted repeat

ABSTRACT
Aim. To design the maps of matched and mismatched potential hairpin structures in the genomes of human and animal coronaviruses. Methods. Bioinformatic analysis of coronaviruses nucleotide sequences, atomic force microscopy. Results. Thermodynamically stable matched and mismatched inverted repeats forming hairpin structures that can appear in genomic RNA of the human and animal coronaviruses (severe acute respiratory syndrome virus, murine hepatitis virus, porcine epidemic diarrhea virus, transmissible gastroenteritis virus and bovine coronavirus) are determined. The maps of hairpin localization (which are a part of the genome signaling mechanisms) are obtained for the genome of coronaviruses. Conclusions. The genes encoding replicase and spike glycoproteins of coronaviruses are the main sites of the localization of potential conservative structural motives. The hairpins are shown to be conservative structural elements inside the set of coronavirus isolates of one species
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