RF Compare allows comparing RF Fold-inferred secondary structures, with a reference of known secondary structures, reporting for each comparison the PPV (Positive Predictive Value, the fraction of basepairs present in the predicted structure that are also present in the reference structure) and the sensitivity (the fraction of base-pairs present in the reference structure that are also in the predicted structure).
Reference structures must be provided in Vienna format:


RF Compare can be invoked both on a single structure, or on an entire folder of RF Fold-predicted structure files. Structures can be provided either in CT or Vienna (dot-bracket) format.


To list the required parameters, simply type:

$ rf-compare -h
Parameter Type Description
-r or --reference string Path to a file containing reference structures in Vienna format (dot-bracket)
-x or --relaxed Uses relaxed criteria (described in Deigan et al., 2009) to calculate PPV and sensitivity
-kn or --keep-noncanonical Keeps non-canonical basepairs in reference structure
-kp or --keep-pseudoknots Keeps pseudoknotted basepairs in reference structure
-kl or --keep-lonelypairs Keeps lonely basepairs (helices of length 1 bp) in reference structure