Skip to main content

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

From: Structural features based genome-wide characterization and prediction of nucleosome organization

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
  1. 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