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Table 1 Performance of TFBS prediction methods using JASPAR.2010 PWMs

From: Evaluating tools for transcription factor binding site prediction

  Sn PPV ACC g FPR s
CLUSTER     
Baycis 0.599 0.497 0.545 0.040
Cister 0.635 0.565 0.599 0.037
MCast 0.774 0.682 0.726 0.032
Comet 0.682 0.589 0.634 0.037
ClusterBuster 0.656 0.580 0.617 0.036
INDIVIDUAL     
Matrix-Scan 0.647 0.579 0.612 0.027
Clover 0.674 0.584 0.627 0.022
FIMO 0.816 0.734 0.774 0.015
Patser 0.723 0.653 0.687 0.016
PossumSearch 0.708 0.635 0.670 0.019
  1. Average sensitivities (Sn), Positive Predictive Value (PPV) and geometric accuracy (ACC g ) are reported together with the false positive rate using scrambled sequences (FPR s ). The best-performing tools, MCast and FIMO are highlighted in bold. Performance was evaluated using the 14 PWMs in the PAZAR-J dataset