Table 2 Performance metrics for genome scans
From: Genome-wide prediction, display and refinement of binding sites with information theory-based models
Execution time (hrs) * | Number of sites found^ | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Site | Length | Weight matrix version | Num. sites in Model | R i,min | R seq | Mosix | Scyld | R i ≥ R i,min | R i ≥ R Seq | Unique Promoters with R i ≥ R seq | Promoters with multiple sites (%) R i ≥ R seq |
PXR | 23 | 1 | 15 | 7.1 | 17.1 | 6.5 | 4.3 | 3.48e5 | 218 | 200 | 8.3 |
PXR | 23 | 2 | 19 | 7.1 | 17.0 | 6 | 3.5 | 4.97e5 | 391 | 365 | 6.6 |
PXR | 23 | 3 | 32 | 7.1 | 14.9 | 7.1 | 4 | 1.10e6 | 3393 | 3036 | 10.5 |
PXR | 23 | 4 | 48 | 7.1 | 14.4 | 6.8 | 3.8 | 1.44e6 | 7694 | 6439 | 16.3 |
NF-κB | 10 | 3 | 75 | 2.6 | 10.9 | 5.8 | - | 1.16e7 | 74050 | 33340 | 54.9 |
AHR | 17 | 1 | 30 | 2.8 | 9.4 | 6.3 | - | 1.20e7 | 42487 | 24764 | 41.7 |
Acc | 28 | 12 | 1.08e5 | 2.4 | 7.4 | 14.5 | - | 4.87e7 | - | - | - |
Don | 7 | 5 | 1.11e5 | 2.4 | 6.7 | 10.5 | - | 4.85e7 | - | - | - |
SC35 | 8 | 1 | 30 | 0.4 | 3.6 | 19 | - | 1.07e8 | - | - | - |