@hackage RNAdesign0.0.2.1

Multi-target RNA sequence design

Categories
- Bioinformatics
License
GPL-3.0-only
Maintainer
choener@tbi.univie.ac.at
Links
- Documentation
- No source repository
- Security
Versions
- 0.1.2.2 Thu, 13 Feb 2014
- 0.1.2.1 Thu, 13 Feb 2014
- 0.1.1.0 Mon, 3 Feb 2014
- 0.1.0.0 Fri, 13 Dec 2013
- 0.0.2.1 Fri, 6 Dec 2013

Installation
In your cabal file:
Dependencies (22)
- array >=0.4
- base >=4 && <5
- containers
- parallel >=3.2
- parsec >=3
- primitive >=0.5
Dependents (1)
@hackage/acme-everything

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

@hackage RNAdesign0.0.2.1

Categories

License

Maintainer

Links

Versions

Installation

Dependencies (22)

Dependents (1)