Here, an extension of the single sequence prediction method DotKnot was presented based on the pairwise comparison of structure elements. This approach called DotKnot-PW is designed as an algorithm for finding the structure including H-type pseudoknots common to two sequences. As shown in Table 1 , DotKnot-PW can greatly improve structure predictions for RNA families when compared with the single sequence prediction using DotKnot. In some cases, a comparative approach might have lower sensitivity than a single sequence prediction; however, this should not generally be judged as 'inferior'. For example, ncRNAs might preserve some integral base pairs throughout evolution and only these will be detected by a comparative approach, which returns the set of base pairs common to a set of evolutionarily related sequences. DotKnot-PW uses a set of unaligned sequences as the input; therefore, no expert user intervention is required. In the future, DotKnot-PW will be extended to include intramolecular kissing hairpins. Furthermore, constrained folding will be implemented to predict a structure subject to constraints, e.g. enforce certain base pairs or regions, which must remain unpaired.