Secondary Structure Prediction for Aligned RNA Sequences

Ivo l. Hofacker, Martin Fekete and Peter F. Stadler

Working Papers from Santa Fe Institute

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.

Keywords: RNA secondary structure prediction; conserved substructures; compensatory mutations (search for similar items in EconPapers)
Date: 2001-11
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Persistent link: https://EconPapers.repec.org/RePEc:wop:safiwp:01-11-067

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