HYDROID (HYDroxyl-Radical fOotprinting Interpretation for DNA) is a python package for the analysis of the experimental data generated by hydroxyl-radical footprinting (HRF) of DNA-protein complexes and its interpretation through comparison to theoretical predictions from molecular models.


HYDROID features


For detailed documentation - click here.

HYDROID video tutorial is available here.

Quick-start guide

NOTE: HYDROID is a full featured Python-script driven software solution that requires basic familiarity with Python-scripting.

HYROID_GUI is a sister package that wraps some basic gel lane quantification functionality into a more user friendly graphical interface. HYDROID_GUI video tutorial is available here.

Quick installation

Install Miniconda with Python2.7 for your platform from https://conda.io/miniconda.html.

NB: As of 2020 only the legacy version 4.3.31 of the Miniconda installer works that can be downloaded from https://repo.anaconda.com/miniconda/

conda install -c hydroid hydroid


HYDROID_test_exp #Tests exeprimental data analysis module
HYDROID_test_pred #Tests molecular structure analysis module (currently supported on Linux and OSX)

For alternative installation instructions for Linux, MacOS and PC see INSTALL.md.

Start by downloading and modifying an example

cd example1
python exp_s2_assign_peaks.py

See full examples set and instructions in examples folder.


Please cite HYDROID using following publication: