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Updated: Jan 19, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Characterization of internal ribosome entry sites according to secondary structure analysis to classify border
Massimo Giangaspero1, Falko Steinbach2, Rebecca Strong2
1Faculty of Veterinary Medicine, University of Teramo, Italy.
Abstract:
Applying palindromic nucleotide substitutions (PNS) method, variable loci of the internal ribosome entry site (IRES) secondary structure in the 5' untranslated region (UTR) of Border disease virus sequences were analysed allowing their allocation into ten IRES classes within the species. Sequence characteristics of Turkish and Chinese strains were highly divergent from other genogroups, indicating geographic segregation and micro-evolutive steps within the species. Observed heterogeneity in the BDV species has to be considered for potential implications on diagnostic tests, control and preventive measures.
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