  Several algorithms for RNA inverse folding have been used to design synthetic
riboswitches, ribozymes and thermoswitches, whose activity has been
experimentally validated. The RNAiFold software is unique among approaches for
inverse folding in that (exhaustive) constraint programming is used instead of
heuristic methods. For that reason, RNAiFold can generate all sequences that
fold into the target structure, or determine that there is no solution.
RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now
defunct COMET language to C++. The new code properly extends the capabilities
of its predecessor by providing a user-friendly pipeline to design synthetic
constructs having the functionality of given Rfam families. In addition, the
new software supports amino acid constraints, even for proteins translated in
different reading frames from overlapping coding sequences; moreover, structure
compatibility/incompatibility constraints have been expanded. With these
features, RNAiFold 2.0 allows the user to design single RNA molecules as well
as hybridization complexes of two RNA molecules.
  The web server, source code and linux binaries are publicly accessible at
http://bioinformatics.bc.edu/clotelab/RNAiFold2.0
