A H-type pseudoknot has two pseudoknot stems S 1 and S 2 . The prerequisite for a conserved pseudoknot pair is that both core H-type pseudoknot stem pairs [S 1 (x), S 1 (y)] and [S 2 (x), S 2 (y)] are significant. The base pair similarity score for two H-type pseudoknots p i (x) and p j (y) in sequences Seq x and Seq y , respectively, is the sum of base pair similarity scores for the core pseudoknot stems as well as the base pair similarity score from a gapped local alignment of the recursive secondary structure elements in the loops (as described for multiloops). A pseudoknot p i (x) in sequence Seq x and a pseudoknot p j (y) in sequence Seq y are a significant pseudoknot pair if the similarity score sim[p i (x), p j (y)] has an estimated P-value less than .