HYDROID

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.

HRF

HYDROID features

Documentation

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.

conda install -c hydroid hydroid

Test 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

HYDROID_get_ex1
cd example1
python exp_s2_assign_peaks.py
...

See full examples set and instructions in examples folder.

Citing HYDROID

Please cite HYDROID using following publication: