Introduction

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/.

Publications

  1. A folding algorithm for extended RNA secondary structures.
    Cite this
    Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL, 2011-07-01 - Bioinformatics (Oxford, England)
  2. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
    Cite this
    Parisien M, Major F, 2008-03-01 - Nature

Credits

  1. Christian Höner zu Siederdissen
    Developer

  2. Stephan H Bernhart
    Developer

  3. Peter F Stadler
    Developer

  4. Ivo L Hofacker
    Investigator

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Summary
AccessionBT000377
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByIvo L Hofacker