Table 3.
Genome-wide performance comparison among the Segal method, N-score, NuPoP, the Random method, the HMM method, DLaNe based on twelve individual structural features and the meta DLaNe method combing six features with the cutoff L = 35
| Structural features | Prediction performance | |||
|---|---|---|---|---|
| Se | Sp | F-measure | Improvement(%) | |
| DNA denaturation | 0.703 | 0.412 | 0.520 | 18.47 |
| Propeller twist | 0.699 | 0.409 | 0.516 | 17.68 |
| DNA-bending stiffness | 0.702 | 0.408 | 0.516 | 17.68 |
| Duplex disrupt energy | 0.625 | 0.394 | 0.483 | 10.21 |
| Bendability | 0.623 | 0.391 | 0.480 | 9.56 |
| Z-DNA | 0.702 | 0.411 | 0.518 | 18.23 |
| Stacking energy | 0.695 | 0.408 | 0.514 | 17.25 |
| Duplex free energy | 0.689 | 0.404 | 0.509 | 16.15 |
| Aphilicity | 0.675 | 0.403 | 0.505 | 15.09 |
| B-DNA twist | 0.654 | 0.384 | 0.484 | 10.34 |
| Protein-DNA twist | 0.652 | 0.381 | 0.481 | 9.67 |
| Protein deformation | 0.526 | 0.353 | 0.422 | -3.66 |
| Meta DLaNe method | 0.734 | 0.457 | 0.563 | 28.45 |
| HMM method | 0.723 | 0.445 | 0.551 | 25.63 |
| Segal method | 0.474 | 0.408 | 0.439 | 0.00 |
| NuPoP method | 0.356 | 0.489 | 0.412 | -6.04 |
| N-score method | 0.317 | 0.439 | 0.368 | -16.05 |
| Random method | 0.346 | 0.346 | 0.346 | -21.10 |
The accuracy of a predicted nucleosome position is measured by sensitivity (Se), specificity (Sp) and F-measure. The improvement of F-measure is computed by comparing with the performance of the pioneer method (Segal method). For DLaNe method, the performance of all 12 structural features is shown in two part, according to their relationship with nucleosome occupancy