Relationship between specificity and sensitivity for PR predictions with overlap criteria λ = 75%. (A) Specificity–sensitivity curves averaged over cross-validation test subsets for different sequence types (for color code, see inset). PRs that contained more than one sequence type were assigned to the type comprising the majority of the prediction. (B) Specificity at the nucleotide level as calculated for each position within a prediction. Deleted nucleotides and SNP positions were assigned a distance of 0. A cumulative histogram of these distances is displayed, showing that, e.g., more than 90% of all nucleotides in PR predictions are within six nucleotides to a known polymorphism. The dotted black line indicates the relationship expected by chance (i.e., predictions were assigned to random genomic locations for calculating distances).
