Abstract
A total of 4051 suboptimal secondary structures are predicted by folding the 5′ non-coding region of ten polioviruses, five human rhinoviruses and three coxsackieviruses using our new suboptimal folding algorithm for the prediction of both optimal and suboptimal RNA secondary structures. A comparative analysis of these RNA secondary structures reveals the conservation of common secondary structure that can be supported by phylogenetic data. The thermodynamic stability and statistical significance of these predicted, conserved helical elements are assessed and significant structure motifs in the 5′ non-coding region are proposed. The possible roles of these structure motifs in the virus life cycle are discussed.
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