Alignment scores as a function of the number of TFBSs in the target window. Trend lines for correct (solid green line) and incorrect (solid red line) alignments; (black dotted line) perfectly separates correct from incorrect alignments. (Inset) The receiver operating characteristic (ROC) curve for the linear SVM classifier separating orthologous from control alignments; the curve profiles the performance in terms of the number of orthologous sequences that are correctly identified among all orthologous sequences (TPR), and the number of control sequences that are incorrectly identified as orthologs among all control sequences (FPR). Gray dotted lines show the standard deviation. The red dotted line displays the ROC curve for a random classifier. The solid red lines indicate the selected operating point (FPR = 0.5).
