Secondary structure prediction for aligned RNA sequences |
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Authors: | Hofacker Ivo L Fekete Martin Stadler Peter F |
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Institution: | Institut für Theoretische Chemie, Universit?t Wien, W?hringerstrasse 17, Austria. |
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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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Keywords: | RNA secondary structure prediction conserved substructures compensatory mutations |
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