Tutorials - 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:

>>> ./runAllNBCalcs.sh

For each example, this will generate the following outputs in the Outputs/ 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 ipython notebook from the command line as follows:

>>> ipython notebook SCA_G.ipynb

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

Tutorials - Examples:

• SCA6.0 - The G protein family
• SCA6.0 - The S1A Serine Proteases
• SCA6.0 - The DHFR (dihydrofolate reductase) family
• SCA6.0 - The Beta-lactamase enzyme family