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All molecular visualizations were obtained using the PyMOL graphic tool (The PyMOL molecular graphics system, Version 1.3r1. Schrodinger, LLC).
All images were obtained using the PyMOL Molecular Graphics System.
3D representation of molecular structures was obtained using the PyMOL Molecular Graphics System http://www.pymol.org.org
The yeast nucleosome structures shown in Figure 6 were obtained using the PyMOL Molecular Graphics System, Version 1.5.0.3 Schrödinger, LLC using structural information obtained in a previous study (White et al. 2001) and available at the Research Collaboratory for Structural Bioinformatics protein data bank (PDB ID 1id3).
The element geometric transformation matrix was obtained using the theory of computer graphics.
The graphics were obtained using Rheoplus.
Graphics were obtained using the plotting system ggplot2 for R. To estimate the ROH from re-sequencing data, we followed the procedure implemented by Bosse et el.
24 The combined binding of the target protein PF0847 with SAM (S-adenosyl-l-methionine), genticin and 16S rRNA A-site was obtained using PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4, Schrödinger, LLC).
Pairwise D' values, r2 values and their graphic representation were obtained using Haploview software at the default settings [ 19].
Graphics and statistics were obtained using the R package (R Development Core Team 2008).
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