Many genes are controlled by small regulatory motifs in their 5' and 3' UTR. For some of these motifs, not the sequence but the secondary structure is important for proper function. It is often difficult to find these small motifs using sequence based methods, due to their low sequence conservation. A more appropriate way is the calculation of a local RNA structure alignment, i.e. to search for the most similar substructures inside larger RNA secondary structures.

This task can be done with the RNAforester [Hoechsmann et al. 2003, Hoechsmann et al. 2004] which can compute global, as well as local RNA structural alignments.