Darn is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM,snoRNA C/D-box and tRNA search.
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M. Zytnicki, C. Gaspin, T. Schiex.
Darn – A Weighted Constraint Solver for RNA Motif Localization.
Constraints, Volume 13 (2008).