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