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

3D structure and RNA secondary structure of two across-bulged motifs and a GAAA-11nt motif. (A) Motif VI, a representative case from 6ERI PDB-entry (see Table 2). (B) Motif VIII, a representative case from 6ERI PDB-entry (see Table 2). (C) GAAA-11nt motif from 2R8S PDB-entry, chain R, involving A-minor A152|C223–G250. Base pairs of stems and adenines of 11 nt-loop are shown in gray. Base-triples are shown in yellow. A-minor adenines are shown in blue. Bulged bases are shown in purple.