Fig. 1 Representation of a pseudoknotted RNA structure.
(A) Arc repre-sentation of base pairs.
(B) Simplified arc representation, in which an arc represents a stem.
(C) Layout of the stems in the lower halfplane to ensure that their backbone direction change from up to down. The stems in the upper halfplane are simply marked with arcs without considering the backbone direction.
(D) Layout of the stems in the upper halfplane to ensure that their backbone direction changes from down to up.
(E) A final visualization of the pseudoknotted RNA structure.