README.md

seqalign

Collection of sequence alignment algorithms.

Table of contents

• Getting started
• Aligners
• Defaults
• Usage
• Alignment result

Getting started

Install the package from npm:

$ npm install --save seqalign

Import the package in your project:

const { NWaligner, SWaligner } = require('seqalign');

Aligners

SWaligner and NWaligner are factory fucntions, you can create many aligners with different parameters and re-use each one multiple times. An aligner is configurable with the following parameters (all of them are optional):

• similarityScoreFunction: takes two characters (string) as input and returns a similarity score (integer).
• gapScoreFunction:
  • Smith-Waterman: takes one positive integer as input (gap length) and returns a score (integer).
  • Needleman-Wunsch: takes no input and returns a constant score used for scoring insertions and deletions in the alignment.
• gapSymbol: a custom character (string) used to represent gaps in the alignment.

All the listed parameters are accessible from each aligner instance in addition with the following non configurable parameters:

• directions: enum object used to define direction codes for the traceback matrix.

Defaults

Here are the default values for the aligner options:

// Smith-Waterman.
const similarityScoreFunction = (char1, char2) => (char1 === char2 ? 2 : -1);
const gapScoreFunction = k => -k;

//Needleman-Wunsch.
const similarityScoreFunction = (char1, char2) => (char1 === char2 ? 1 : -2);
const gapScoreFunction = () => -1;

// Common defaults.
const gapSymbol = '-';

Usage

Instantiating SWaligner or NWaligner returns an aligner object which exposes an align method. align accepts the two strings to align as input:

// Smith-Waterman.
const { SWaligner } = require('seqalign');

const defaultAligner = SWaligner();
const customAligner = SWaligner({
  gapScoreFunction: x => x / 2,
  gapSymbol: '~',
})

const defaultResult = defaultAligner.align('insertion', 'deletion');
const customResult = customAligner.align('insertion', 'deletion');

console.log(defaultResult.alignment)
// > ertion
// > e-tion

console.log(customResult.alignment)
// > inse~~rtion
// > ~~~ele~tion

// Needleman-Wunsch.
const { NWaligner } = require('seqalign');

const defaultAligner = NWaligner();
const customAligner = NWaligner({
  inDelScore: -3,
  gapSymbol: '~',
})

const defaultResult = defaultAligner.align('insertion', 'deletion');
const customResult = customAligner.align('insertion', 'deletion');

console.log(defaultResult.alignment)
// > -inse--rtion
// > d---ele-tion

console.log(customResult.alignment)
// > insertion
// > dele~tion

Alignment result

The align method of the aligner instances returns an object with the following properties:

• score <int>: alignment score.
• originalSequences Array<str>: original input sequences.
• alignedSequences Array<str>: aligned sequences.
• scoringMatrix Array<Array<int>>: alignment scores matrix.
• tracebackMatrix Array<Array<int>>: alignment traceback directions matrix.
• coordinateWalk Array<Array<int>>: coordinate walk from the traceback matrix.
• alignment <str>: printable visual alignment string.