Non-coding RNA play a major role in cellular regulation. It is currently believed that about 80% of the genome is transcribed, but only about 1.3% is translated in protein. Finding common RNA sequence-structure motifs is the major way of assigning function to these elements.
We will discuss different approaches to find common RNA sequence-structure properties and the problems occurring in practical applications (like uncertainty of structure prediction). Albeit the basic pairwise comparison can be done in polynomial time, current approaches are not capable of clustering the huge amount of data, and we will discuss possible approaches to overcome these limitations.