RNAdesign (hackage): 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:  http://dx.doi.org/10.1002/bip.22337
Keywords: bioinformatics|gpl|library|program