Summary of the results of predictions of programs Footer, ConSite and rVista
|
|
Footer |
ConSite (def) |
ConSite (70%) |
rVista |
|---|---|---|---|---|
| No. of sites | 72 | 49 | 49 | 69 |
| TP | 60 | 23 | 34 | 54 |
| FP | 23 | 15 | 28 | 189 |
| SN | 83.3% | 46.9% | 69.4% | 78.2% |
| SP
|
72.3%
|
60.5%
|
54.8%
|
22.2%
|
-
Footer ran with its default parameters (one “seed” site per 300 bp, WAP cutoff 0.05%). ConSite ran with its default parameters and also with 70% for score threshold and the minimum between 70% or the default for identity percentage. rVista ran with the option “conserved”. Based on the results of the optimal runs of these programs on the same promoter set, their sensitivity and specificity values were measured to be 69% and 55% for ConSite (on 49 sites) and 78% and 22% for the rVista (on 69 sites), respectively. By comparison, Footer achieved a sensitivity of 83% and specificity of 72% (on 72 sites).
