Figure 5
From: Structator: fast index-based search for RNA sequence-structure patterns
Bidirectional recursive RSSP matching using an affix array. Procedure bidir-search finds all matches of a given RSSP (P, R), beginning the pattern extensions from any position in the loop region or any position in a completely unpaired pattern. In each call, parameter v denotes the affix-interval representing matches of the pattern substring P[r + 1..r' - 1], 0 ≤ r ≤ r' <m satisfying the structural constraints imposed by R[r + 1..r' - 1]. The procedure takes care to change the search direction only as often as necessary, in particular it changes the direction only once per base pair.