Table 2.
Comparison of performance of seven programs on all 105 MNChIP-seq datasets without running time limit
| Programs | G1 (200 bp) |
G2 (500 bp) |
G3 (1000 bp) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of datasets with the PM found | Ave. no. of motifs found | Ave. no. of known motifsb | Ave. no. of cooperative motifsc | No. of datasets with the PM found | Ave. no. of motifs found | Ave. no. of known motifs | Ave. no. of cooperative motifs | No. of datasets with the PM found | Ave. no. of motifs found | Ave. no. of known motifs | Ave. no. of cooperative motifs | |
| ProSampler | 90 (85.7%) a | 49.6 | 12.9 | 2.7 | 93 (88.6%) | 93.8 | 17.9 | 3.4 | 88 (83.8%) | 119.0 | 17.5 | 3.7 |
| BioProspector | 77 (73.3%) | 150.0 | 8.7 | 0.9 | 75 (71.4%) | 150.0 | 7.9 | 1.1 | 60 (57.1%) | 150.0 | 5.9 | 0.8 |
| DREME | 88 (83.8%) | 22.7 | 8.0 | 2.5 | 90 (85.7%) | 42.1 | 9.0 | 2.4 | 81 (77.1%) | 48.0 | 6.6 | 1.6 |
| XXmotif | 86 (81.9%) | 49.4 | 12.4 | 2.7 | 68 (64.8%) | 50.5 | 10.3 | 2.4 | 42 (40.0%) | 54.3 | 6.4 | 1.5 |
| Homer | 77 (73.3%) | 121.2 | 20.6 | 3.5 | 85 (81.0%) | 136.9 | 18.9 | 3.2 | 89 (84.8%) | 147.1 | 17.0 | 2.8 |
| motifRG | 43 (41.0%) | 126.8 | 9.4 | 1.8 | 46 (43.8%) | 134.6 | 11.5 | 2.0 | 49 (46.7%) | 132.5 | 13.1 | 2.2 |
| Dimont | 68 (64.8%) | 4.3 | 1.6 | 0.6 | 77 (73.3%) | 2.8 | 1.4 | 0.6 | 77 (73.3%) | 2.0 | 1.3 | 0.5 |
a
Numbers in bold type represent the best performance in the column.
b
Average number of predicted motifs matched to those in JASPAR in each dataset.
c
Average number of predicted motifs matched to those in TCoF-DB for the target TF in each dataset.