The results are shown in Table 1 . DotKnot-PW has the highest average MCC of 0.75 for the test sequences. For each reference structure with the 10 support sequences from the corresponding RFAM family, 10 predictions are returned ordered by the combined free energy and similarity score. If only the Fig. 2 . A set of edges with positive scores is given between nodes p 1 ,. . .,p 7 in the first sequence and p 1 ,. . .,p 6 in the second sequence. The goal is to find the best set of non-overlapping structure elements in the two sequences such that the interval ordering is preserved. The optimal structure element alignment, which preserves the interval ordering includes structure elements p 1 , p 4 , p 7 in the first sequence and p 1 , p 4 , p 6 in the second sequence pairwise prediction with highest combined free energy and similarity score is taken, DotKnot-PW has an improved average MCC of 0.81. Tfold and hxmatch have average MCC of 0.6 and 0.59, respectively. CARNAC has average MCC of 0.45 with much higher average specificity than sensitivity. The prediction results for single sequence structure prediction for each of the reference sequences with experimentally determined structures are also shown in Table 1 . Note that this does not include the prediction for the support sequences from RFAM, as no experimentally determined structures are available. All single sequence pseudoknot prediction methods show improved results over using RNAfold. DotKnot has the highest average MCC of 0.76, followed by IPKnot and ProbKnot.