energy landscapes and folding kinetics of nucleic acids
ribolands is a package to compute folding kinetics on dynamic or
bimolecular energy landscapes. It provides wrapper functions for the programs
treekin, which have to installed separately. See
below for an example workflow.
Two scripts for cotranscriptional folding are part of
DrTransformer: Short for "DNA-to-RNA Transformer", the program computes cotranscriptional folding of larger RNAs by generating a heuristic energy landscape at every transcription step.
ViennaRNA packageto calculate transition rates and
treekinto simulate folding kinetics.
echo "CUGCGGCUUUGGCUCUAGCC" | DrTransformer.py --visualize pdf
BarMap: folding kinetics on dynamic energy landscapes. For each sequence length, the coarse-grained barriers landscape is computed. During kinetic simulations, a mapping between subsequent landscapes is used to transfer occupancy from one landscape to the next. This is mostly a reimplementation of
BarMapby Hofacker et al. (2010), but it makes use of more recent functionality of
echo "CUGCGGCUUUGGCUCUAGCC" | BarMap.py --pyplot
ribolands uses RNAsubopt from the ViennaRNA package, barriers and
treekin for landscape computations. Make sure that you have the latest
versions installed, i.e.
barriers-v1.6 and, recommended,
ViennaRNA-v2.2 or later.
- RNA (installed with the ViennaRNA package)
- crnsimulator (https://github.com/bad-ants-fleet/crnsimulator)
>>> from ribolands import sys_subopt_range, sys_suboptimals, sys_barriers, sys_treekin >>> [name, seq] = ['test', 'ACUGAGGUCGAU'] >>> ener, nos = sys_subopt_range(seq, nos=100000) >>> sfile = sys_suboptimals(name, seq, ener=ener) >>> [sfile, bfile, efile, rfile, psfile] = sys_barriers(name, seq, sfile, maxn=50, minh=1.0, rates=True) >>> [tfile, efile] = sys_treekin(name, seq, bfile, rfile, p0=['2=1'], t0=1e-6, t8=1e10)
If you are using
DrTransformer please cite:
- Stefan Badelt. Control of RNA function by conformational design. PhD thesis, University of Vienna, 2016
- BarMap: RNA folding on dynamic energy landscapes Hofacker et al. (2010)
python setup.py install
Development / Unittests
python setup.py test
Build the documentation
sphinx-build -b html docs ~/your/html/sourcedir/