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. 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.
If you find this program useful, please cite:
Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler
A Graph Coloring Approach to Designing Multi-Stable Nucleic Acid Sequences
Biopolymers, 99, 12, 1124-1136, 2013, Wiley
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Modules
- BioInf
- BioInf.RNAdesign
- BioInf.RNAdesign.Assignment
- BioInf.RNAdesign.Graph
- BioInf.RNAdesign.LogMultinomial
- BioInf.RNAdesign.OptParser
- BioInf.RNAdesign
Downloads
- RNAdesign-0.0.2.1.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
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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 |
|---|---|
| Change log | changelog |
| Dependencies | array (>=0.4), base (>=4 && <5), BiobaseTurner (>=0.3.1.1), BiobaseVienna (>=0.3), BiobaseXNA (>=0.7.0.1), cmdargs (>=0.10 && <0.11), containers, fgl (>=5.4), fgl-extras-decompositions (>=0.1.0.0), 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), random (>=1.0), RNAFold (>=1.99.3.3), transformers (>=0.3), tuple (>=0.2), vector (>=0.10), ViennaRNA-bindings (>=0.0.2.3) [details] |
| License | GPL-3.0-only |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@tbi.univie.ac.at |
| Category | Bioinformatics |
| Uploaded | by ChristianHoener at 2013-12-06T23:53:01Z |
| Distributions | |
| Reverse Dependencies | 1 direct, 0 indirect [details] |
| Executables | RNAdesign |
| Downloads | 4520 total (16 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs not available [build log] All reported builds failed as of 2016-12-19 [all 8 reports] |