(a) Direct comparison between relative affinities for 10-mers inferred from PBM intensities by FeatureREDUCE and relative in vivo occupancy at 955 genomic locations of type NNCACGTGNN (E-box with flanks) as measured by ChIP-seq (Zhou and O'Shea, 2011). Trimmed-mean (trim = 10%) ChIP-seq fold-enrichments were computed for all unique 10-mer sequences that occur at least three times in the genome. To account for saturation of higher-affinity binding sites, a basic equilibrium model (green curve) was fit with a single free-protein parameter. Red lines indicate the error between the observed and predicted relative ChIP enrichments. (b) The same plot for the BEEML-PBM algorithm (Zhao and Stormo, 2011). The same equilibrium model (green curve) was fit, but the optimal free protein concentration parameter was much lower than in (a), so the saturation is not apparent in this case.