SequalJS

SequalJS is a JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation. It allows handling protein and peptide sequences with modifications, useful for proteomics research, mass spectrometry data analysis, and bioinformatics applications.

Features

• Full support for ProForma 2.0 standard for proteoform notation
• Parse complex peptide sequences with modifications
• Handle various modification types:
  • Site-specific modifications
  • Terminal modifications (N-terminal and C-terminal)
  • Global modifications
  • Mass shift modifications
  • Labile modifications
  • Modifications with unknown positions
• Support for advanced ProForma features:
  • INFO tags and metadata
  • Ambiguity groups with localization scores
  • Sequence ambiguities
  • Crosslinks and branches
  • Range modifications
• Precise handling of decimal values in mass shifts

Installation

npm install sequaljs

Usage

Basic Parsing

import { Sequence } from 'sequaljs';

// Parse a simple peptide with modification
const seq = Sequence.fromProforma('ELVIS[Phospho]K');
console.log(seq.seq[4].value); // "S"
console.log(seq.seq[4].mods[0].modValue.primaryValue); // "Phospho"

// Convert back to ProForma notation
console.log(seq.toProforma()); // "ELVIS[Phospho]K"

Terminal Modifications

import { Sequence } from 'sequaljs';

// N-terminal and C-terminal modifications
const seq = Sequence.fromProforma('[Acetyl]-PEPTIDE-[Amidated]');

// Access N-terminal modification (position -1)
const nTermMod = seq.mods.get(-1);
if (nTermMod) {
  console.log(nTermMod[0].modValue.primaryValue); // "Acetyl"
}

// Access C-terminal modification (position -2)
const cTermMod = seq.mods.get(-2);
if (cTermMod) {
  console.log(cTermMod[0].modValue.primaryValue); // "Amidated"
}

Global Modifications

import { Sequence } from 'sequaljs';

// Global fixed modification
const seq = Sequence.fromProforma('<[Carbamidomethyl]@C>PEPTCDE');
console.log(seq.globalMods[0].modValue.primaryValue); // "Carbamidomethyl"
console.log(seq.globalMods[0].targetResidues); // ["C"]

Working with INFO Tags

import { Sequence } from 'sequaljs';

// Parse sequence with INFO tag
const seq = Sequence.fromProforma('ELVIS[Phospho|INFO:newly discovered]K');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "Phospho"
console.log(mod.infoTags[0]); // "newly discovered"

// Multiple INFO tags
const seq2 = Sequence.fromProforma('ELVIS[Phospho|INFO:newly discovered|INFO:Created on 2021-06]K');
console.log(seq2.seq[4].mods[0].infoTags.length); // 2
console.log(seq2.seq[4].mods[0].infoTags); // ["newly discovered", "Created on 2021-06"]

Joint Representation

import { Sequence } from 'sequaljs';

// Parse sequence with joint interpretation and mass
const seq = Sequence.fromProforma('ELVIS[U:Phospho|+79.966331]K');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "Phospho"
console.log(mod.source); // "U"
console.log(mod.modValue.pipeValues[1].mass); // 79.966331

// With observed mass
const seq2 = Sequence.fromProforma('ELVIS[U:Phospho|Obs:+79.978]K');
const mod2 = seq2.seq[4].mods[0];
console.log(mod2.modValue.primaryValue); // "Phospho"
console.log(mod2.modValue.pipeValues[1].observedMass); // 79.978

Crosslinks and Complex Features

import { Sequence } from 'sequaljs';

// Crosslinks with mass shifts and info tags
const seq = Sequence.fromProforma('PEPTK[XL:DSS#XL1|+138.068|INFO:reaction=NHS]IDE');
const mod = seq.seq[4].mods[0];
console.log(mod.modValue.primaryValue); // "DSS"
console.log(mod.source); // "XL"
console.log(mod.crosslinkId); // "XL1"
console.log(mod.modValue.pipeValues[1].mass); // 138.068
console.log(mod.infoTags[0]); // "reaction=NHS"

// Complex example with multiple modification types
const complex = Sequence.fromProforma(
  'PEP[U:Deamidation|+0.984]T[U:Phospho#1(0.75)|+79.966]K[XL:DSS#XL2]IDE'
);

Gap Notation

import { Sequence } from 'sequaljs';

// Parse sequence with gap of known mass
const seq = Sequence.fromProforma('RTAAX[+367.0537]WT');
console.log(seq.toStrippedString()); // "RTAAXWT"
console.log(seq.seq[4].value); // "X"
console.log(seq.seq[4].mods[0].modType); // "gap"
console.log(seq.seq[4].mods[0].mass); // 367.0537

API Reference

• Sequence.fromProforma(string): Parse a ProForma string into a Sequence object
• sequence.toProforma(): Convert a Sequence object back to a ProForma string
• sequence.toStrippedString(): Get the plain amino acid sequence without modifications
• sequence.seq: Access the individual residues with their modifications
• sequence.mods: Access modifications by position, including terminal modifications
• sequence.globalMods: Access global modifications
• sequence.sequenceAmbiguities: Access sequence ambiguity information

License

MIT