Characteristics and Prediction of RNA Structure

Algorithm 1

(1) For (i = startLen, i ≤ sequence length)

   (1.1) Run the basic prediction algorithm of secondary structures to produce

   matrix Z, and trace back Z to obtain a base pair list L.

   (1.2) Identify all helices in L, and combine helices separated by small internal

   loops or bulges.

   (1.3) Assign a score to each helix by summing up the scores of its constitutive

   base pairs or stacks. Select the helix H according to helix length and score,

   and merge H into the base pair list S to be reported.

   (1.4) Remove positions of H from the initial sequence.

   (1.5) Assign next golden point to i.

   End for

(2) Compute pseudoknots on the remaining sequences by the crossing of two

   subsequences. Trace back to obtain a base pair list K and merge K into S.

(3) Report the base pair list S and terminate.