Aligning Covariance Models

While RNA primary structure describes solely the string of bases, RNA secondary structure includes local intra-molecular interactions between pairs of bases, which form weak hydrogen bonds. Two such bonded bases are called paired. Thus RNA secondary structure can be represented as a sequence of bases annotated with lines between paired bases. A more intuitive representation displays RNA secondary structure in a two-dimensional format with paired bases forming stems and unpaired bases forming loops. Finally secondary structures without crossing pairs can be represented in a tree format. All three representations are shown in Figure 1.