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

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


Gan et al. BMC Bioinformatics 2012 13:49   doi:10.1186/1471-2105-13-49

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