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A folding algorithm for extended RNA secondary structures.

ABSTRACT: MOTIVATION: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. RESULTS: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. AVAILABILITY: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

SUBMITTER: Honer zu Siederdissen C

PROVIDER: S-EPMC3117358 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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A folding algorithm for extended RNA secondary structures.

Höner zu Siederdissen Christian C Bernhart Stephan H SH Stadler Peter F PF Hofacker Ivo L IL

Bioinformatics (Oxford, England) 20110701 13

<h4>Motivation</h4>RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.<h4>Results</h4>We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of program ...[more]

PMID: 21685061

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