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Table 1 Twelve structural features of DNA sequences, and genome-wide correlation coefficients between in vitro and in vivo experimental nucleosome occupancies [9, 45] and structural profiles of 12 features

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

Structural features Description Pearson correlation
   In vitro[9] In vivo[9] In vivo[45]
Propeller twist [29] The angle of the two aromatic bases in a base pair. 0.82 0.67 0.35
DNA denaturation [35] The ability of DNA to denature. 0.77 0.61 0.34
DNA-bending stiffness [33] The anisotropic flexibility of DNA. 0.72 0.56 0.35
Bendability [31] The trinucleotide bendability. 0.63 0.51 0.15
Duplex disrupt energy [38] DNA duplex energy. 0.57 0.40 0.21
Stacking energy [34] Energy scale of dinucleotide base-stacking energy scale. -0.80 -0.63 -0.35
Z-DNA [37] The ability to be covered from B-to Z-DNA -0.78 -0.61 -0.36
Duplex free energy [39] The thermodynamic energy content. -0.74 -0.57 -0.33
Aphilicity [36] The free energy values for a transition from B- to A-DNA form. -0.69 -0.54 -0.27
Protein-DNA twist [32] The ability to be deformed by protein. -0.52 -0.42 -0.16
B-DNA twist [30] The mean twist angles in B-DNA. -0.17 -0.11 -0.08
Protein-induced deformation [32] The ability to be changed by proteins. -0.09 -0.06 -0.02