The Program RNAinverse

RNAinverse searches for sequences folding into a predefined structure, thereby inverting the folding algorithm. Input consists of the target structures (in dot-bracket notation) and a starting sequence, which is optional.

Lower case characters in the start sequence indicate fixed positions, i.e. they can be used to add sequence constraints. 'N's in the starting sequence will be replaced by a random nucleotide. For each search the best sequence found and its Hamming distance to the start sequence are printed to stdout. If the the search was unsuccessful a structure distance to the target is appended.

By default the program stops as soon as it finds a sequence that has the target as MFE structure. The option -Fp switches RNAinverse to the partition function mode where the probability of the target structure $\exp(-E(S)/RT)/Q$ is maximized. This tends to produce sequences with a more well-defined structure. This probability is written in dot-brackets after the found sequence and Hamming distance. With the option -R you can specify how often the search should be repeated.