# Usage¶

We provide tutorials that walk through the process of sector identification for three protein families: the Ras-like small G-proteins, the metabolic enzyme Dihydrofolate Reductase (DHFR), and the antibiotic resistance enzyme Beta-lactamase.

To run the SCA calculations for all three examples, you can execute the following shell script from the scripts/ directory:

./runAllNBCalcs.sh


For each example, this will generate the following outputs in the output/ directory:

1. A pickle database (*.db file) that contains the results of the calculations (these are then read in and analyzed in the IPython notebooks - *.ipynb)

2. A *.log file that provides some information about the analysis

3. A processed alignment (*.fasta file) resulting from the scaProcessMSA script.

Following this step, you can begin the tutorial as an interactive Jupyter notebook from the command line as follows:

jupyter notebook SCA_G.ipynb


This should open the notebook in a browser window, where you can run the code, and examine the SCA results.