A folding algorithm for extended RNA secondary structures

Bioinformatics. 2011 Jul 1;27(13):i129-36. doi: 10.1093/bioinformatics/btr220.


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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Pairing
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA / genetics
  • Sequence Analysis, RNA
  • Software


  • RNA