. Author manuscript; available in PMC: 2019 Apr 1.

Published in final edited form as: Nat Protoc. 2018 Nov;13(11):2535–2556. doi: 10.1038/s41596-018-0048-z

Table 1.

Main HYDROID functions and their description.

HYDROIDexp library
assign_peaks_interactive	Provides interactive interface for a semi-automated algorithm used to identify positions of peaks on gel lane profiles.
call_peaks_interactive	Provides interactive interface to assign individual peaks with respect to DNA sequence position.
fit_peaks	Main function that fits a mathematical model to the gel lane profile and evaluates DNA cleavage intensities.
plot_prof_on_seq	Plots any data profile along the DNA sequence and allows for normalization and fitting of two or more profiles.
simulate_gel	Simulates the shape of gel lane profile and infers a gel lane image based on H-SASA profile.
HYDROIDpred library
get_DNA_H_SASA	Estimates theoretical DNA cleavage profiles (H-SASA profiles) from a DNA-protein structure