Introduction to alignment-js

alignment-js is a powerful JavaScript library designed to facilitate seamless alignment and manipulation of data structures. This comprehensive guide explores various APIs provided by alignment-js with practical code snippets.

Getting Started

Install the library using npm:

  npm install alignment-js

Basic Alignment API

The align function allows you to align two sequences:

  
    const { align } = require('alignment-js');
    const seq1 = 'GATTACA';
    const seq2 = 'GCATGCU';
    const result = align(seq1, seq2);
    console.log(result);
  

Custom Scoring Function

You can define a custom scoring function for the alignment:

  
    const scoring = (a, b) => (a === b ? 1 : -1);
    const result = align(seq1, seq2, { scoringFunction: scoring });
    console.log(result);
  

Global Alignment

Perform global alignment using the Needleman-Wunsch algorithm:

  
    const { globalAlign } = require('alignment-js');
    const result = globalAlign(seq1, seq2);
    console.log(result);
  

Local Alignment

Perform local alignment using the Smith-Waterman algorithm:

  
    const { localAlign } = require('alignment-js');
    const result = localAlign(seq1, seq2);
    console.log(result);
  

Adding Custom Gap Penalties

Include custom gap penalties for alignment:

  
    const options = {
      gapOpen: -2,
      gapExtend: -1,
    };
    const result = globalAlign(seq1, seq2, options);
    console.log(result);
  

App Example

Let’s build a simple app that aligns DNA sequences using the discussed APIs:

  
    const express = require('express');
    const { align, globalAlign, localAlign } = require('alignment-js');

    const app = express();

    app.get('/align', (req, res) => {
      const { seq1, seq2 } = req.query;
      const result = align(seq1, seq2);
      res.send(result);
    });

    app.get('/globalAlign', (req, res) => {
      const { seq1, seq2 } = req.query;
      const result = globalAlign(seq1, seq2);
      res.send(result);
    });

    app.get('/localAlign', (req, res) => {
      const { seq1, seq2 } = req.query;
      const result = localAlign(seq1, seq2);
      res.send(result);
    });

    app.listen(3000, () => {
      console.log('App listening on port 3000');
    });
  

This simple app provides APIs to perform basic, global, and local alignments of DNA sequences.

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