RNA sequence design software
Requirements: python, pycosat, RNAlib (from the ViennaRNA package)
usage: python DesiRNA -f [input filename] [options]
-s SET, --set SET Name of a file containing set of the preferred motifs.
-m NUMBER_OF_MUTATIONS, --mutations NUMBER_OF_MUTATIONS Number of mutation cycles.
-v {0,1}, --verbose {0,1} Displaying solution from SATsolver.
-p PROB, --probability PROB Probability of mutating the whole fragment from library of motifs.
-c {0,1}, --complex {0,1} Include RNA-RNA complex formation in DesiRNA scoring function.
-n NUMBER_SEQ, --number_of_sequences NUMBER_SEQ Number of best sequences to return.
with the example.fas structured as:
> structure 1
[RNA secondary structure in dot-bracket notation]
> structure 2
[RNA secondary structure in dot-bracket notation]
...
[RNA squence constraints in IUPAC notation]
prevented [1st prevented RNA subsequence in IUPAC notation]
prevented [2nd prevented RNA subsequence in IUPAC notation]
...