Many pseudoknot prediction programs have been evaluated using all the entries in the PseudoBase database (van Batenburg et al., 2000) . There are several caveats in this approach. First, the sequences given in PseudoBase are those which exactly harbor the pseudoknot. However, in practice structure prediction algorithms will be applied to longer sequences without prior knowledge of the pseudoknot location. Second, long-range pseudoknot entries appear in a truncated version in the database. Third, some classes of pseudoknots have a large number of entries (such as short H-type pseudoknots in the 3 0 -untranslated regions of plant viruses), whereas more complex types of pseudoknots only have one representative (such as long-range rRNA pseudoknots). Therefore, a hand-curated dataset of pseudoknot structures will be used here.