RNAdesign: Multi-target RNA sequence design
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
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- RNAdesign-0.1.2.2.tar.gz [browse] (Cabal source package)
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Versions [RSS] | 0.0.2.1, 0.1.0.0, 0.1.1.0, 0.1.2.1, 0.1.2.2 |
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Change log | changelog |
Dependencies | array (>=0.4), base (>=4 && <5), BiobaseTurner (>=0.3.1.1), BiobaseVienna (>=0.3), BiobaseXNA (>=0.8.1), bytestring (>=0.10), cmdargs (>=0.10 && <0.11), 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 && <0.0.3), 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) [details] |
License | GPL-3.0-only |
Copyright | Christian Hoener zu Siederdissen, 2013-2014 |
Author | Christian Hoener zu Siederdissen |
Maintainer | choener@tbi.univie.ac.at |
Category | Bioinformatics |
Uploaded | by ChristianHoener at 2014-02-13T23:55:24Z |
Distributions | |
Reverse Dependencies | 1 direct, 0 indirect [details] |
Executables | RNAdesign |
Downloads | 4540 total (7 in the last 30 days) |
Rating | (no votes yet) [estimated by Bayesian average] |
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Status | Docs available [build log] Successful builds reported [all 1 reports] |