is returned for the corresponding stem s i . A MWIS calculation on the candidate list returns the set of internal stems with maximum weight in linear time (56) . The outer stem s i can, therefore, become an interrupted stem s L i with bulges and internal loops or the exterior stem of a multiloop. The sum of confidences serves as the updated weight for outer stem s i . After the whole endpoints list has been scanned, stems interrupted by bulge loops or internal loops are stored in a new dictionary D L s . Multiloops are stored in a separate dictionary D M s . As a last step, the free energies of the interrupted stems and multiloops are evaluated with the tool RNAeval (11) . Only structure elements with negative free energy are stored.