Protease dictionary

A numba compatible dictionary that stores different regular expressions for proteolytic enzymes. The dictionary is identical to the one in AlphaPept and was largely taken from the Pyteomics website which in turn derived the rules are from expasy.

protease_dict["trypsin"]

'([KR](?=[^P]))'

Get proteolytic cleavage sites for a protein sequence

get_cleavage_sites[source]

get_cleavage_sites(sequence:str, protease:str)

Function to get the position of proteolytic cleavage sites in a sequence.

Args: sequence (str): Amino acid sequence. protease (str): Protease to use for in silico digestion. Returns: list: List of cleavage site indices for the selected protease.