A Folding Algorithm for Extended RNA Secondary Structures

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/.

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Authors
  • Höner zu Siederdissen, Christian
  • Berhart, Stephan H.
  • Stadler, Peter F.
  • Hofacker, Ivo L.
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Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Subjects
Angewandte Informatik Sonstiges
Journal or Publication Title
ISMB
Publisher
Oxford University Press
Page Range
i129-i136
Number
Volume
27
Date
2011
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