Figure 9.

The results of a comparison of 14 motif-detection programs on a benchmark study [17]. At the nucleotide level, sensitivity (nSn), positive predictive value (nPPV), performance coefficient (nPC), and correlation coefficient (nCC) were measured. With nTP, nFN, nFP and nTN as nucleotide-level true positive, false negative, false positive, and true negative, respectively, nSn = nTP/(nTP + nFN); nPPV = nTP/(nTP + nFP); nPC = nTP/(nTP + nFN + nFP); and nCC = (nTP·nTN - nFN·nFP)/. At the site level, sensitivity (sSn), positive predictive value (sPPV), and average site performance (sASP) were measured. With sTP, sFN, sFP as site-level true positive, false negative, and false positive, respectively, sSn = sTP/(sTP + sFN); sPPV) = sTP/(sTP + sFP; and sASP = (sSn + sPPV)/2.