Purpose:

COMET (COmprehensive Motif Evaluation Toolkit) was developed to process high-throughput datasets for the evaluation of enzymatic specificity.

The process involves multiple stages to refine a comprehensive substrate profile as illustrated below:

Installation:

Clone the GitHub with the terminal command:

git clone https://github.com/Collinformatics/COMET

Then move to the COMET directory:

cd COMET

Create conda environment:

conda env create -f environment.yml

Host Website

Activate conda environment:

conda activate comet

You can start up the website with:

python app.py

• This will generate a URL with an ip address and port, it should be http://127.0.0.1:9090
  • Click on the link to go to the website, or enter the address in a browser.

Testing The Program:

Processing DNA:

• To test the program a trial dataset is available in the folder:

  data/validation/
  

Troubleshooting:

Unterminated processes can result in the website not starting correctly.

Two possible solutions are:

1. Automated Fix:

   To fix this problem, execute this command to terminate the python processes:

    ./killServer.sh
   

   If you host the website at a port other than 9090, add the port to the command:

    ./killServer.sh <port>
   

2. Manual Fix:

   List Open Files at port 9090 to find relevant process IDs:

    lsof -i :9090
   

   Kill these processes:

    kill <process ID>