Loop extrusion assay by DNA and SMC (LEADS)
Single-molecule assay for DNA loop extrusion by SMC. Kymograph and kinetics from the loop assays.
Project Details
Installation
It's best to use an isolated environment for this program. But it might just work with your standard/base environment if it has python>=3.7.
You can create an environment in conda by running the following line in a terminal
conda create -n leads-env python=3.8Then activate the environment by
conda activate leads-envYou can install the LEADS module by dowloading this repo. Go to the folder containing setup file in terminal and install by the following commands.
Install all the dpendencies
pip install -r requirements.txtAnd then install the leads program
python setup.py installUsage
From a terminal or command prompt
Activate environment in a terminal
conda activate leads-envTo open the gui of kymograph analysis
python -m leads.gui.kymograph_guiTo open the gui for cropping large number of image files in a folder
python -m leads.gui.crop_images_guiAlternative
If you are in windows os, you can double click the bat script files LEADS_kymoGUI.bat for the kymo program and LEADS_cropGUI.bat for the cropping program.
Contributing
Please use issues to post your bugs and send pull requests to merge your modifications/improvemnts.
All the contributors will be acknowledged here and will be included if this ends up in a publication.
Authors & Contributors
List of contributors:
- Biswajit Pradhan (biswajitp145_at_gmail.com)
- Roman Barth
Pubslihed articles based on this module
SMC complexes can traverse physical roadblocks bigger than their ring size, Cell Reports, 2022
Condensin-driven loop extrusion on supercoiled DNA. nature structural molecular biology, 2022
The Smc5/6 complex is a DNA loop extruding motor. Nature(under review), 2022