RNAdesign: Multi-target RNA sequence design

[ bioinformatics, gpl, library, program ] [ Propose Tags ]

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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  • BioInf
    • BioInf.RNAdesign
      • BioInf.RNAdesign.Assignment
      • BioInf.RNAdesign.Graph
      • BioInf.RNAdesign.LogMultinomial
      • BioInf.RNAdesign.OptParser

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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
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Reverse Dependencies 1 direct, 0 indirect [details]
Executables RNAdesign
Downloads 4520 total (16 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-12-19 [all 8 reports]

Readme for RNAdesign-0.0.2.1

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