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.
- 2 in 1: HRF experimental data quantification + theoretical analysis of atomistic structures
- Extracts cleavage intensities at individual DNA nucleotides by a number of constraint fitting algorithms
- Uses both Gaussian and Lorentzian models for band intensities
- Cross-platform python-scripted solution, can be install on Linux, MacOS, Windows
- Completely free and relies on open source components such as ImageJ and FreeSASA
- Provides examples of raw data analysis together with data analysis workflows.
For detailed documentation - click here.
HYDROID video tutorial is available here.
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.
Install Miniconda with Python2.7 for your platform from https://conda.io/miniconda.html.
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
See full examples set and instructions in examples folder.
Please cite HYDROID using following publication:
- A.K. Shaytan, H. Xiao, G.A. Armeev, D.A. Gaykalova, G.A. Komarova, C. Wu, V.M. Studitsky, D. Landsman, A.R. Panchenko “Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID”, Nature Protocols, 2018, DOI: 10.1038/s41596-018-0048-z