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
