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Project · science

LEADS

Loop Extrusion Assay by DNA and SMC. A Python GUI for kymographs and loop kinetics from single-molecule movies, used across several SMC papers.

Status
stable
Started
Aug 2020
Tags
  • python
  • gui
  • single-molecule
  • image analysis
LEADS graphical interface showing a fluorescence image of DNA and the kymograph extracted from it

LEADS turns single-molecule movies of DNA loop extrusion into kymographs, and kymographs into loop sizes and kinetics, through a Python graphical interface.

I started it at TU Delft in 2020, and it was used to analyse loop-extrusion and roadblock data, for example in SMC complexes can traverse physical roadblocks bigger than their ring size (released on Zenodo, Pradhan, Barth and Analikwu, 2023). The Kim lab at the Max Planck Institute of Biophysics maintains its own version.

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