Using our novel tool, RNAdesign, we make it possible to efficienctly design multi-stable RNA sequences. RNAdesign combines a graph-coloring based approach with a sampling method that allows us to explore the space of candidate sequences for the given structural designs very efficiently.
You can read about RNAdesign here: ‘Höner zu Siederdissen et al. (2013)’.
The sources also available via hackage and github. Additional scripts, and example structural targets are on github as well.
An archive (sources, executables, structural targets, additional scripts) is here, but hackage and github
The images below show three (very small) target structures and the ViennaRNA dotplot (far right) for the designed sequence.
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local list of references
Christian Höner zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, and Peter F. Stadler. 2013. Computational design of RNAs with complex energy landscapes. Biopolymers 99, no. 12. 99: 1124–36. doi:10.1002/bip.22337.