Extended RNA Secondary Structure: RNAwolf

We are currently working on integration of non-canonical base-pairs into RNA secondary structure prediction. A simplified (non-nearest-neighbor) model is described in Höner zu Siederdissen et al. (2011), and is used by us to determine features that are important for prediction.

The current software is beyond the state described in the paper and includes a rich scoring model. It is part of a rewrite of my base libraries.

RNAwolf, MC-Fold-DP, and SSPcompare

RNA Secondary Structure: ViennaRNA 2.0

In Lorenz et al. (2011) we describe the newest version of the main software by the TBI, the ViennaRNA 2.0 package. Ronny Lorenz is the main author and maintainer. If you want to convert Turner parameters to the ViennaRNA format, the sources for the ViennaConverter are on hackage. If you want a precompiled binary, mail me (or type “cabal update && cabal install BiobaseVienna”).

local list of references

Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011. A folding algorithm for extended RNA secondary structures. Bioinformatics 27, no. 13. 27: 129–36. doi:10.1093/bioinformatics/btr220.

Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, and Ivo L. Hofacker. 2011. ViennaRNA package 2.0. Algorithms for Molecular Biology 6, no. 26. 6. doi:10.1186/1748-7188-6-26.