Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors

The secondary structure of the lysine riboswitch from PDB entry 3D0U. The structure is visualized with VARNA (Darty et al. 2009). Loops are assigned with their types, classes, and confining stems. A-minor A124–A20–G66 of type X is emphasized on the structure and presented separately with the 3D structure of its nucleotides in red, green, and blue. Each nucleotide of the A-minor is annotated with the element of RNA secondary structure. Each nucleotide pair is annotated with their relative positions within the secondary structure.