cascleave-lookup

Requirements:

• Python >3.0
• Python packages noted in requirements.txt
• (preferred) Gmail account

How to use?

• Script #1: lookup_c.py -- this will take a list of GenInfo Identifiers (gi #s), retrieve their associated amino acid sequences from NCBI, and then run them through the CasCleave algorithm hosted by Kyoto University. You will need to change Entrez.email = "******@*****.***" to your email. Make sure you have an NCBI account with this email, and expect to recieve cascleave results at this email address soon after the script completes its run.
• Script #2: process_email_output_c.py -- this will login to your Gmail (change email_id = '****@*****.***'), asking you for your password (not stored anywhere!!!), and spit out a list of protein names, predicted cut sites, and sequences of those sites. It will also compare those sites with sites found via our proteomics pipeline (Unique_FDR_CC.csv).

Caveats

• This code utilizes web scraping and simple email libraries -- if either the CasCleave algorithm website or Gmail change their interfaces, this script will cease to function.

Citation:

Victor KG, Heffron DS, Sokolowski JD, Majumdar U, Leblanc A, Mandell JW. Proteomic identification of synaptic caspase substrates. Synapse. 2018; 72(1).