Pseudoknots are functional elements in RNA structures and therefore, the most promising approach for comparative prediction is a structure comparison with less focus on exact sequence matching. In fact, perfect conservation on the sequence level can be more of a curse than a blessing. Especially ncRNAs are known to evolve quickly and so-called consistent and compensatory base pairs in both sequences will give much more confidence for structure conservation than a sequence alignment. One strong point of the DotKnot method for single sequence pseudoknot prediction (Sperschneider and Datta, 2010; Sperschneider et al., 2011) is that the set of possible H-type pseudoknot candidates (and secondary structure elements) is explicitly computed and thus readily available for further investigation. The main steps in the pairwise pseudoknot prediction approach DotKnot-PW are as follows ( Fig. 1) :