peptide-cutter

Peptide Cutter

A library for in silico proteolytic digestion of proteins and peptides.

View on npm here.

Installation

npm install peptide-cutter --save

PLEASE NOTE

This module relies on positive lookbehind regex and thus can only be run with newer versions of JavaScript. You may need to use the --harmony argument with node in order to use this module.

Also note

v2.x.x introduces breaking changes from v1.x.x in the return format

Usage

var peptideCutter = require('peptide-cutter');

var options = {
  'enzyme': 'trypsin',
  'num_missed_cleavages': 2,
  'min_length': 2,
  'max_length': 30
};

var cutter = new peptideCutter(options);

var peptides = cutter.cleave("KARATE");

Return format:

[ { sequence: 'KAR', start: 0, end: 2, missed: 1 },
  { sequence: 'KARATE', start: 0, end: 5, missed: 2 },
  { sequence: 'AR', start: 1, end: 2, missed: 0 },
  { sequence: 'ARATE', start: 1, end: 5, missed: 1 },
  { sequence: 'ATE', start: 3, end: 5, missed: 0 } ]

• sequence is the digested fragment
• start is the 0-based index of where in the original sequence the fragment can be found
• end is the 0-based index of where in the original sequence the fragment ends (this value is inclusive)
• missed is the number of missed cleavages found in this particular fragment.

About

The regex for the cleavage sites was stolen borrowed from the Pyteomics package which in turn comes from the Expasy PeptideCutter.

Available enzymes

• arg-c
• asp-n
• bnps-skatole
• caspase 1-10
• chymotrypsin high specificity
• chymotrypsin low specificity
• clostripain
• cnbr
• enterokinase
• factor xa
• formic acid
• glutamyl endopeptidase
• granzyme b
• hydroxylamine
• iodosobenzoic acid
• lysc
• ntcb
• pepsin ph1.3
• pepsin ph2.0
• proline endopeptidase
• proteinase k
• staphylococcal peptidase i
• thermolysin
• thrombin
• trypsin

The available enzymes and their corresponding regex are also found in expasy_rules.json

Tests

You can run npm test to run the tests after installing the development dependencies. There are basic tests to make sure all the enzymes will cleave proteins, but I cannot guarantee their completeness.

Future functionality

There are currently no planned improvements to this module. I am open to suggestions so let me know if you think something is missing.

License

This software is released under the MIT license

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