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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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