The set of recursive H-type pseudoknots stored in dictionary D p will certainly contain false positive pseudoknots. Therefore, a MWIS calculation with local free energy weights is employed using the structure elements from all four dictionaries: D s , D L s , D M s and D p . Stems s i 2 D s need to have confidence cðs i Þ > 1 Â E À3 to participate (55) . Furthermore, stems are allowed to contain nested structure elements, including pseudoknots. The MWIS procedure with nesting is described in detail in KnotSeeker (39) . Note that we do not include the free energy gain of À1:5 kcal/mol for the outer loop as in KnotSeeker, because favourable nested structures are already included through dictionaries D L s and D M s .