Measuring retrieval accuracy. Motif retrieval accuracy is estimated using simulated JASPAR motifs, as described in the text. The figure plots the percentage of correct query-target pairs (true positives) as a function of the percentage of incorrect pairs (false positives) as we traverse the list of query-target pairs sorted by Tomtom P value or any of the other three methods of combining column-wise scores. The solid and dashed lines correspond to width-normalized scores scores (P values, arithmetic mean, and geometric mean), and the green dotted line represents sum of column scores. This figure is for euclidean distance (ED) at a sampling rate of S/8.