The RNAdesign package

[Tags: gpl, library, program]

The RNA sequence design problem asks for a single sequence that readily folds into the (one or more) structural targets that are given as input.

This program expects on standard input a file with one or more structures and, possibly, additional sequence constraints in the form of an IUPAC string. It will then run a Markov chain to find a sequence that is optimal with regard to the structural targets and the user-defineable optimization function.

The user can give different optimization criteria on the command line, akin to a simple calculator.

For more details please consult: https://github.com/choener/RNAdesign/blob/master/README.md

You can also run RNAdesign --showmanual which will display the same README.md.

If you find this program useful, please cite:

Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler
Computational design of RNAs with complex energy landscapes
2013. Biopolymers. 99, no. 12. 99. 1124–36.

http://dx.doi.org/10.1002/bip.22337


Properties

Versions0.0.2.1, 0.1.0.0, 0.1.1.0, 0.1.2.1, 0.1.2.2
Dependenciesarray (>=0.4), base (==4.*), BiobaseTurner (>=0.3.1.1), BiobaseVienna (>=0.3), BiobaseXNA (>=0.8.1), bytestring (>=0.10), cmdargs (==0.10.*), containers, fgl (>=5.4), fgl-extras-decompositions (>=0.1.0.0), file-embed (>=0.0.6), lens (>=3.9), monad-primitive (>=0.1), mwc-random-monad (>=0.6), parallel (>=3.2), parsec (>=3), ParsecTools (==0.0.2.*), primitive (>=0.5), PrimitiveArray (>=0.5.3), random (>=1.0), RNAFold (>=1.99.3.3), transformers (>=0.3), tuple (>=0.2), vector (>=0.10), ViennaRNA-bindings (>=0.1.1.1)
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2013-2014
AuthorChristian Hoener zu Siederdissen
Maintainerchoener@tbi.univie.ac.at
Stabilityexperimental
CategoryBioinformatics
ExecutablesRNAdesign
Upload dateThu Feb 13 23:55:24 UTC 2014
Uploaded byChristianHoener
Downloads360 total (25 in last 30 days)

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