Local structures can be predicted by a modified version of the
fold() algorithm that restricts the span of all base pairs.
The local analog to
fold(). Computes the minimum free energy structure including only base pairs with a span smaller than
pfl_fold computes partition functions for every window of size winSize possible in a RNA molecule, allowing only pairs with a span smaller than pairSize. It returns the mean pair probabilities averaged over all windows containing the pair in pl. winSize should always be >= pairSize. Note that in contrast to
Lfold(), bases outside of the window do not influence the structure at all. Only probabilities higher than cutoff are kept.
If pup is supplied (i.e is not the NULL pointer),
pfl_fold()will also compute the mean probability that regions of length
uare unpaired. The parameter
uis supplied in pup. On return the pup array will contain these probabilities, with the entry on pup[x] containing the mean probability that x and the
u-1preceding bases are unpaired. The pup array needs to be large enough to hold
n+1float entries, where
nis the sequence length.
init_pf_fold(). length is the length of the sequence.