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项目作者： ncbi

项目描述 ：
Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes
高级语言： Python
项目地址: git://github.com/ncbi/HYDROID.git
创建时间： 2017-06-02T20:59:08Z
项目社区：https://github.com/ncbi/HYDROID
开源协议：Other
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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

  • 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.

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.

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/

  1. conda install -c hydroid hydroid

Test HYDROID:

  1. HYDROID_test_exp #Tests exeprimental data analysis module
  2. 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

  1. HYDROID_get_ex1
  2. cd example1
  3. python exp_s2_assign_peaks.py
  4. ...

See full examples set and instructions in examples folder.

Citing HYDROID

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