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Secondary structure prediction for aligned RNA sequences.

Ivo L Hofacker·Martin Fekete·Peter F Stadler
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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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AlgorithmsArchaeaBase SequenceConsensus SequenceDatabases, Nucleic AcidEscherichia coliEvolution, MolecularMolecular Sequence DataNucleic Acid ConformationPhylogenyProkaryotic CellsRNARNA StabilityRNA, Ribosomal, 16SRNA, Ribosomal, 23SSequence AlignmentSequence Homology, Nucleic AcidThermodynamicsJournal ArticleResearch Support, Non-U.S. Gov't

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Ivo L Hofacker, Martin Fekete, Peter F Stadler. 2002-06-21. Secondary structure prediction for aligned RNA sequences.. https://doi.org/10.1016/s0022-2836(02)00308-x

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