RNA secondary structure example. Schematic representation of the secondary structure for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; the RNA STRAND ID for this molecule is ASE_00199. Solid grey lines represent the ribose-phosphate backbone. Dotted grey lines represent missing nucleotides. Solid circles mark base pairs. Dashed boxes mark structural features. We define an RNA secondary structure as a set of base pairs . In this work, we consider all C-G, A-U and G-U base pairs as canonical, and all other base pairs as non-canonical. However, we note that from the point of view of the planar edge-to-edge hydrogen bonding interaction , there are C-G, A-U and G-U base pairs that do not interact via Watson-Crick edges, and vice-versa [14, 42]. Comparative sequence analysis tools do not currently describe bond types. A number of structural motifs can be identified in a secondary structure: A stem is composed of one or more consecutive base pairs. A hairpin loop contains one closing base pair, and all the bases between the paired bases are unpaired. An internal loop is a loop with two closing base pairs, and all bases between them are unpaired. A bulge loop can be seen as a variant of an internal loop in which there are no unpaired bases on one side. A multi-loop is a loop which has at least three closing base pairs; stems emanating from these base pairs are called multi-loop branches. A pseudoknot is a structural motif that involves non-nested, crossing base pairs.