Supplementary Figure 1: Comparison of various fitting methods and band-shape models applied to the analysis of an HRF gel lane profile. | Nature Protocols

Supplementary Figure 1: Comparison of various fitting methods and band-shape models applied to the analysis of an HRF gel lane profile.

From: Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Supplementary Figure 1

Results of HYDROIDexp Stage 4 are presented for different combinations of band shape models (Gaussian and Lorentzian) and constrained fitting methods. Data are taken from an HRF experiment on S. cerevisiae centromeric nucleosome reconstituted on 601TA sequence (Example 1). Application of constrained fitting methods dramatically improves the quality of the fitted solution. A combination of Gaussian band shapes and “dSIGMA>= 0” constraint options provides the best fitting quality while presenting a physically plausible solution. The x-axis corresponds to the distance along the gel lane in pixels. The y-axis shows the intensity of the pixels along the gel lane profile.

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