RNAwolf and MC-Fold-DP are two programs (rather, collections of a library and several programs, each) that deal with RNA secondary structure prediction. Both are described in Höner zu Siederdissen et al. (2011) and available from this site, together with more information, some data, and source code. SSPcompare is a modest tool to help compare different RNA folding algorithms.
With RNAwolf we aim to refine RNA secondary structures to extended RNA secondary structures. An extended structure contains not only the six canonical basepair types AU UA GC CG UG GU but all 4x4 possible pairs. Each nucleotide can be engaged in a pairing using one of the three nucleotide edges: Watson-Crick, Sugar, or Hoogsteen. It follows, that a nucleotide can now be engaged in more than one pairing at the same time. RNAwolf aims to predict such structures. We hope to use such predictions as a stepping-stone towards full 3D structure prediction.
For more details, follow the link.
MC-Fold-DP is a re-implementation of Parisien and Major (2008) with substantial algorithmic changes. The original algorithm has a run-time of O(n15 / 2), wich quickly becomes infeasible to use once the input size n exceeds 100 nucleotides. The grammar behind our re-implementation is unambigious which means that one can calculate:
For more details, follow the link.
SSPcompare is a modest tool that takes a library of known sequence-structure pairs, e.g. Andronescu et al. (2008), and predictions by different algorithms and produces tables for easy comparison of different programs. It was written to automate the rather tedious procedure of comparing and testing different programs. The library behind this tool can be of interest if you want to train folding algorithms and need a way to quickly ascertain training success.
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Andronescu, Mirela, Vera Bereg, Holger Hoos, and Anne Condon. 2008. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 9: 340. doi:10.1186/1471-2105-9-340. http://www.biomedcentral.com/1471-2105/9/340.
Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011. A Folding Algorithm for Extended RNA Secondary Structures. Bioinformatics 27: 129–36. doi:10.1093/bioinformatics/btr220.
Parisien, Marc, and Francois Major. 2008. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452: 51–55. doi:10.1038/nature06684.