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Analysis code for Shen et al. 2022

This repository contains original code used to analyze data for the Shen et. al. 2022 paper.

Each directory contains a different part of the analysis

  • md_sim_pattern_matching/ contains code to match footprinting and TEN-map data against patterns from MD simulations
  • pvalues_calcs/ contains code to generate p-values for how well the MD simulation matches the footprinting and TEN-map data
  • modeling/ contains code for using sequence, structure, and electrostatic features to predict H-NS DBD binding locations at the bp level
  • compare_ishihama_data/ contains code for checking for enrichment of sequence, structure, and electrostatic features in gSELEX data from the Ishihama group.

Each directory has it's own README.md file describing what it contains and how to re-run the analysis.

For any specific questions about this code or analysis please contact Michael Wolfe at mwolfe6@wisc.edu.
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