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

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