RNAmotifs allows you to predict a structural motif common to a set of RNA sequences. The resulting motifs includes information on both RNA sequence and structure. Motifs are described both graphically and by a data file containing information on the underlying probabilistic model.
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Rabani et. al,
Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes,
Proc Natl Acad Sci U S A., September 2008