rnaifold is a web server that solves the RNA inverse folding problem, using constraint programming. Given a target RNA secondary structure, as well as optional nucleotide constraints, RNAiFold determines all (or a large number of) RNA sequences, whose minimum free energy structure is the target structure.
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RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Garcia-Martin JA, Dotu I, Clote P.
Nucleic Acids Res. 2015 May 27. pii: gkv460.
RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design
J.A. Garcia-Martin, P. Clote, I. Dotu,
Journal of Bioinformatics and Computational Biology ,DOI: 10.1142/S0219720013500017