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sub-cut

Tool to find which proteases cut a substrate based on sequence

Descreption

The MEROPS database is an information resource for peptidases and their substrates. I created this tool to refine the search for proteases that will cut a given peptide. sub-cut will sort all the database's proteases based on the similarity of the provided substrate sequence with the substrates that it's known to cut.

The protease-substrate data from MEROPS db are stored locally but I also provide them processed in the .data/substrates.data.json file.

Usage

  • Pass the sequences that you want cut in data/target_peptides.fasta.
  • Set the specificity threshold in sub-cut.py
  • Run sub-cut.py
python3 sub-cut.py
  • Check your results in data/<current_date_and_time>_results.xlsx
  • Check out analyses.ipynb for more info and example.ipynb for an example