Several of the test sequences contain pseudoknots where one of the core pseudoknot stems is interrupted by bulges or internal loops: Escherichia coli tmRNA, Legionella pneumophila tmRNA, the SARS frameshifting pseudoknot, human telomerase and Tetrahymena telomerase. For all of these pseudoknots, DotKnot delivers the best results in terms of sensitivity and specificity. For example, the Tetrahymena telomerase RNA (TER) contains a pseudoknot with a conserved central GA bulge in one of its stems, which is vital for telomerase function (76) . DotKnot perfectly predicts this bulged pseudoknot, while all other methods do not predict a pseudoknot structure. The biological relevance of pseudoknots with bulged residues should not be underestimated. Therefore, a prediction algorithm that can handle pseudoknots with interrupted stems such as DotKnot is highly desirable.