RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform
Fig 2
Algorithm execution for one example sequence which requires two steps.
(Step 1) From the correlation cor(k), we select one peak which corresponds to a position lag k. Then, we search for the largest stem and form it. Two fragments, “In” (the interior part of the stem) and “Out” (the exterior part of the stem), are left, but only the “Out” may contain a new stem to add. (Step 2) The procedure is called recursively on the “Out” sequence fragment only. The correlation cor(k) between the “Out” fragment and its mirror is then computed and analyzing the k positional lags allows to form a new stem. Finally, no more stem can be formed on the fragment left (colored in blue), so the procedure stops.