/HYDROID

Python package for analyzing hydroxyl-radical footprinting experiments of protein-DNA complexes
  1. Python 100.0%
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example1 Added function for electrophoresis gel simulation (#2) Aug 14, 2017
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HYDROIDexp.py
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README.md

HYDROID

HYDROID (HYDroxyl-Radical fOotprinting Interpretation for DNA) is a python package for the analysis of experimental data generated by hydroxyl-radical footprinting (HRF) of DNA-protein complexes.

HRF

Workflow

This package has two python libraries implementing complementary functionalities:

  • HYDROIDexp.py - extraction of DNA cleavage frequency profiles from gel electrophoresis images.
  • HYDROIDpred.py - estimation of theoretical DNA cleavage frequency profiles from PDB structures through estimating deoxyribose hydrogen atoms solvent accessibility (H-SASA).

WF

Documentation

Several step-by-step examples serve as a manual to the package.

  • Example 1: Quantifying HRF of a centromeric nucleosome with DNA radioactively labeled at 3' end. Predicting cleavage frequency profiles from an atomistic structure model and comparing to experimental ones.
  • Example 2: Quantifying HRF of a nucleosome with DNA radioactively labeled at 5' end. Highlights conversion of gel images to data profiles via ImageJ.

Video tutorial is available here.

DocString documentation for every function is provided inside the libraries and step-by-step example python files.

Detailed information about HYDROID algorithms can be found in the accompanying publication: A.K. Shaytan et al. (in preparation)

Installation

Latest stable version of HYDROID can be downloaded from the releases page. The name of the directory containing the contents of the package should always be HYDROID.

Requirements

  • Python 2.7
  • Python modules specified in requirements.txt.
  • freesasa library v2.0.1 should be compiled with python bindings and accessible in python (only needed for HYDROIDpred).

Installation examples

Installing Python and its modules is usually system specific. Using virtualenv together with pip or other python package managers to match the exact versions of the modules is recommended. We provide environment files for pip (requirements.txt) and Continuum Anaconda (conda_env.yml).

INSTALL.md provides common installation examples for Linux, MacOS and PC.

Citing HYDROID

Please cite HYDROID using following publication:

  • A.K. Shaytan et al. (in preparation)

Further information

HYDROID is intended to help in quantification of hydroxyl-radical footprinting experiments of protein-DNA complexes (or free DNA) and comparison of these data to available structural models.

Hydroxyl-radical footprinting is one of DNA footprinting methods.

For the initial familiarization with hydroxyl-radical footprinting techniques and theory following references and references therein are suggested: