The key point of the DotKnot-PW approach is how to score the similarity of stems, secondary structure elements and H-type pseudoknot candidates derived from sequences Seq x and Seq y . Related work has been done for stem finding in unaligned sequences, where stem candidates are assigned a matching score across unaligned sequences, e.g. in SCARNA. Another point is how to assess the significance of a similarity score using Pvalues. These points will be explained in detail in the following section.