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NUPACK-based Concentration Plots

Setup

  • Download and compile Nupack 3 and set the NUPACKHOME environment variable to the nupack root directory
  • Install python requirements via pip install -r requirements.txt

Usage

You can make a set of plots for a single sequence by running

python plot_conc_space.py [SEQUENCE] R105_states.txt -o output.png -t [TITLE]

The R105_states.txt specifies the input and reporter sequences as well as which complexes to include in the calculation.