sequence-alignment-js

Sequence Alignment Algorithms implemented in Javascript, with a command line application.

The core algorithm in this package, which is the space efficient version of Gotoh's algorithm, is based on Eugene W. Myers and Webb Miller (1988) Optimal alignments in linear space, Bioinformatics 4, 11-17.

Installation

npm i -g sequence-alignment

Usage

Help

Use align -h to show help page.

Examples

Global, Semiglobal and Local Alignment

Global alignment of DNA sequences, using default parameters of NCBI megablast (match = 1, mismatch = -2, gap = linear)

$ align ATCCGAACATCCAATCGAAGC AGCATGCAAT
ATCCGAACAT-CCAATCGAAGC
||||||||||||||||||||||
A---G--CATGC-AAT------
score: -4

Semiglobal and local alignment using -M s and -M l, respectively

$ align -M s ATCCGAACATCCAATCGAAGC AGCATGCAAT
ATCCGAACATC-CAA-TCGAAGC
|||||||||||||||||||||||
------AGC-ATGCAAT------
score: 5

$ align -M l ATCCGAACATCCAATCGAAGC AGCATGCAAT
A-CAT-CCAAT
|||||||||||
AGCATGC-AAT
score: 5

DNA/RNA/Protein

Use the -d, -r, -p flags to specify the type of sequence to be DNA, RNA and protein, respectively. Defaults to DNA.

# DNA
align ACCGGT ACGCAT
align -d ACCGGT ACGCAT
# RNA
align -r AUGCGU AUGCUG
# protein
align -p ACGHKL ACGLKL

Specifying Substitution Matrix or Match/Mismatch Scores

Use the -m option to specify the substitution matrix (usually for aligning protein sequences) OR match/mismatch scores (usually for DNA/RNA sequences).

# align protein sequences using BLOSUM62 matrix
align -p -m blosum62 ASDFG ASDGF

# align DNA sequences with match=2; mismatch=-1
align -d -m 2,-1 ACGTA AGTAC

Gap Penalty

If you used a matrix such as BLOSUM62, the gap

The gap penalty should be a positive number.

Use a single number to specify a constant (linear) gap penalty.

$ align ACCGGT AT -m 5,-1 -g 3
ACCGGT
||||||
A----T
score: -2

Use a pair of numbers to specify the gap open penalty and gap extend penalty, so that the affine gap penalty is used.

$ align ACCGGT AT -m 5,-1 -g 3,1
ACCGGT
||||||
A----T
score: 3