Finding potential binding sites with RNAduplex

If the sequences are very long (many kb)RNAcofold is too slow to be useful. The RNAduplex program is a fast alternative, that works by predicting only intermolecular base pairs. It's almost as fast as simple sequence alignment, but much more accurate than a BLAST search.

The example below searches the 3' UTR of an mRNA for a miRNA binding site.