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  • Title: Secondary structure prediction for aligned RNA sequences.
    Author: Hofacker IL, Fekete M, Stadler PF.
    Journal: J Mol Biol; 2002 Jun 21; 319(5):1059-66. PubMed ID: 12079347.
    Abstract:
    Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.
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