Boltzman sampling of RNA secondary structures with support of pseudoknots of type genus 1 (1-structures).
To compile and run it, do: <edit the variable VIENNARNA in file Makefile.am to point to your distribution of ViennaRNA package (http://www.tbi.univie.ac.at/RNA/)> aclocal autoconf automake --add-missing ./configure make src/gfold
Firstly done by Fenix Huang as a part of paper: Topology and prediction of RNA pseudoknots (Reidys, Christian M. and Huang, Fenix W. D. and Andersen, Jørgen E. and Penner, Robert C. and Stadler, Peter F. and Nebel, Markus E.) published in Bioinformatics 2011
Updated and extended by Marcel Kucharik.
In case you have found a good use of it, don't hesitate to cite:
@article{Reidys15042011, author = {Reidys, Christian M. and Huang, Fenix W. D. and Andersen, Jørgen E. and Penner, Robert C. and Stadler, Peter F. and Nebel, Markus E.}, title = {Topology and prediction of RNA pseudoknots}, volume = {27}, number = {8}, pages = {1076-1085}, year = {2011}, doi = {10.1093/bioinformatics/btr090}, abstract ={Motivation: Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered.Results: Here, we use the natural topological classification of RNA structures in terms of irreducible components that are embeddable in the surfaces of fixed genus. We add to the conventional secondary structures four building blocks of genus one in order to construct certain structures of arbitrarily high genus. A corresponding unambiguous multiple context-free grammar provides an efficient dynamic programming approach for energy minimization, partition function and stochastic sampling. It admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10–20% compared with earlier approaches. More general models based on building blocks of higher genus are also discussed.Availability: The source code of gfold is freely available at http://www.combinatorics.cn/cbpc/gfold.tar.gz.Contact: duck@santafe.eduSupplementary information: Supplementary data are available at Bioinformatics online.}, URL = {http://bioinformatics.oxfordjournals.org/content/27/8/1076.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/27/8/1076.full.pdf+html}, journal = {Bioinformatics} }