switch.pl

The switch.pl script can be used to design bi-stable structures, i.e. structures with two almost equally good foldings. For two given structures there are always a lot of sequences compatible with both structures. If both structures are reasonable stable you can find sequences where both target structures have almost equal energy and all other structures have much higher energies. Combined with RNAsubopt, barriers and treekin this is a very useful tool for designing RNAswitches.

The input requires two structures in dot-bracket notation and additionally you can add a sequence. It is also possible to calculate the switching function at two different temperatures with option -T and -T2.