Sequence Design

1. Prepare an input file inv.in containing the target structure and sequence constraints

     (((.(((....))).)))
     NNNgNNNNNNNNNNaNNN
   

2. Design sequences using RNAinverse

   	$ RNAinverse < inv.in
   	GCCgGGCAUCGGUUaGGC    7
   
   	$ RNAinverse -R5 -Fp < inv.in
   	GGUgGGACAUCUCCaACU    4
   	CCCgCGGGUUACCGaGGG   11  (0.960708)
   	UGUgCGUGAUAACGaACA    7
   	CCGgGCCGAAAGGUaUGG    9  (0.895937)
   	CGGgAGCUUUGGCUaUCG    6
   	CCCgCCCGGAAGGGaGGG   11  (0.963131)
   	GAUgCCAUAAUUGGaAUC    5
   	CCCgCCCUAAUGGGaGGG    5  (0.963027)
   	GGUgGCUCAGCAGUaAUC    4
   	CCCgCCCUAAUGGGaGGG   14  (0.963027)
   

The output consists of the calculated sequence and the number of mutations needed to get the MFE-structure from the start sequence (start sequence not shown). Additionaly, with the partition function folding (-Fp) set, the second output is another refinement so that the ensemble preferes the MFE and folds into your given structure with a distinct probability, shown in brackets.

Another useful program for inverse folding is RNA designer, see http://www.rnasoft.ca/. RNA Designer takes a secondary structure description as input and returns an RNA strand that is likely to fold in the given secondary structure.