Pseudoknots are functional structure elements, which have been reported in most classes of RNA (15) . A pseudoknot forms when unpaired bases in a loop pair with complementary bases in a single-stranded region outside the loop (Figure 1 ). Pseudoknots play key roles in viral genome replication and regulation of protein synthesis (16) . Pseudoknots are also found in the cell where they participate in processes such as splicing, ribosomal frameshifting, telomerase activity and ribosome function (17) (18) (19) . In many cases, they assist in the overall 3D folding (20, 21) and should not be excluded from computational structure prediction.