Accuracy of several variants of pWALTZ-like scoring.

The method described as “original PSSM” uses the pWALTZ PSSM; “scrambled PSSM” averages over all permutations of the positions of the PSSM; “scrambled hexamers” first scrambles the hexamers from which the PSSM is constructed; “scrambled prion domain” tests the ability of the original PSSM to detect scrambled versions of the prion domain. Accuracy is measured using the area under the receiver operating characteristic curve (AUC-ROC) and the area under the precision recall curve (AUC-PR). All methods use a filtering step that considers only regions with negative FoldIndex scores and Q/N content of at least 25%. Figure A in S1 File provides the ROC and PR curves corresponding to these results, and Table A in S1 File provides additional results when no pre-filtering is performed.