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J Mol Biol. 2002 Jun 21;319(5):1059-66.

Secondary structure prediction for aligned RNA sequences.

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1
Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, Austria.

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.

PMID:
12079347
DOI:
10.1016/S0022-2836(02)00308-X
[Indexed for MEDLINE]
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