Global, semi-global and local alignment implemented in Javascript.
The simplest way to align two sequences is to import the align function from the align module. The three possible types of alignment are global, local and semi.
const align = require('align');
var alignment = align('ataggcgata', 'ggcg', type='global');
console.log(alignment.to_string());
console.log(alignment.get_score());
alignment = align('ataggcgata', 'ggcg', type='local');
console.log(alignment.to_string());
console.log(alignment.get_score());
alignment = align('ataggcgata', 'ggcg', type='semi');
console.log(alignment.to_string());
console.log(alignment.get_score());If you want to perform multiple alignments you can create an Aligner. You can specify the type of alignment when instantiating the Aligner. Again, the three possibilities are 'global', 'local' and 'semi'. The default is 'global'.
const Aligner = require('align').Aligner;
// instantiate a global aligner
var global_aligner = new Aligner();
global_aligner = new Aligner('global');
// instantiate a local aligner
var local_aligner = new Aligner('local');
// instantiate a semi-global aligner
var semi_global_aligner = new Aligner('semi');Custom alphabets and scoring matrices can be created used. You will need to defined your own CharacterMap for a new alphabet.
const align = require('align');
var character_map = new align.CharacterMap('abcde');
var scoring_matrix = new Int32Array([
5, 4, 3, 2, 1,
4, 5, 4, 3, 2,
3, 4, 5, 4, 3,
2, 3, 4, 5, 4,
1, 2, 3, 4, 5
]);
var aligner = new align.Aligner('local', scoring_matrix, character_map);
var alignment = aligner.align('abcdef', 'aecbfabefacbfe');
console.log(alignment.to_string());
console.log(alignment.get_score());Examples can be found in the examples directory.