Based on the anisotropic deformation of DNA structure in nucleosomes, the non-linear dimensionality reduction algorithm Isomap is used to derive a structural signal accounting for most structural variances from the DNA structural data of nucleosome crystals. The analysis of this structural signal by continuous wavelet transform has successfully revealed the common regularity of nucleosome DNA deformation and also the peculiarity of structural configurations in nucleosomes with particular histone or DNA composition, or special ligands. The relationship between the constituent dinucleotides and the signal energy distribution shows that the fluctuation of a structural signal is sensitive to certain dinucleotide types. (C) 2012 Elsevier B.V. All rights reserved.