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Secondary Structure Prediction for Aligned RNA Sequences

2002; Elsevier BV; Volume: 319; Issue: 5 Linguagem: Inglês

10.1016/s0022-2836(02)00308-x

1089-8638

Ivo L. Hofacker, Martin Fekete, Peter F. Stadler,

RNA Research and Splicing

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.