Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Figure 2
(A) The allowed case. The first nucleotides of the left substructures in both sequence 1 and sequence 2 are basepaired, and the first and last nucleotides in the right substructures are basepaired to each other.
(B) A disallowed case. The score of the joined alignment will not be calculated using the bifurcation-loop calculation (the resulting alignment will, however, be calculated by expanding the alignment result from (A). There are two reasons: the first nucleotide of the left substructure in sequence 2 is not basepaired, and the first and the last nucleotides of the right substructures are not basepaired in both sequences.