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Table 2 Performance of the different motif discovery tools using FIMO

From: Evaluating tools for transcription factor binding site prediction

Motif discovery tool Sn PPV ACC g FPR s
ChIPMunk 0.886 0.786 0.834 0.009
HOMER 0.901 0.795 0.846 0.007
MEME-ChIP 0.865 0.771 0.817 0.013
rGADEM 0.933 0.839 0.884 0.002
  1. Average sensitivities (Sn), Positive Predictive Value (PPV), geometric accuracy (ACC g ) and false positive rate on scrambled sequences (FPR s ) are reported. The best-performing tool rGADEM is highlighted in bold. Note that TFBS PWMs were generated only for the 12 transcription factors in the PAZAR-E dataset