SPF (Structural Pattern Finder) is a tool that identify regions of a given RNA or DNA sequence that possess a high probability of being structured. This is achieved by computing, for each region, the difference between the folding free energy of the native sequence with the average folding free energy of randomized sequences of the same base composition.
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I. Barrette, G. Poisson, P. Gendron and F. Major (2000)
Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching,
Nucleic Acids Res. 2001 February 1; 29(3): 753–758.