smith-waterman-wrapper

A simple node module that wraps the functionalities of a smith-waterman implementation written in C

The original program written in C is found here. https://github.com/noporpoise/seq-align

Install

You can install smith-waterman-wrapper by running,

npm install smith-waterman-wrapper

Usage

Align two unaligned sequences

.alignPair( sequence1, sequence2, matchScore, misMatchScore, gapScore, callback )
callback passed (err, data)

const smithW = require('smith-waterman-wrapper');
var sequence1 = 'AADBFGTRHYSRRFDERS';
var sequence2 = 'AADGTDRSYSRFFDERTS';
var matchScore = 1;
var misMatchScore = -1;
var gapScore = -1;

smithW.alignPair(sequence1,sequence2,matchScore,misMatchScore,gapScore,function(err,data){
    if(err){
        console.log(err);
    }else{
        console.log(data);
    }
});

Align 2 sequences and output alignment along with score matrix

.alignPairGetMatrix (sequence1, sequence2, matchScore, misMatchScore, gapScore, callback) callback passed (err, data)

Align sequence file (Read 2 sequences at a time and align them)

.alignFile (inputFile, matchScore, misMatchScore, gapScore, callback) callback passed (err, data)

  const smithW = require('smith-waterman-wrapper');
  var inputFile = 'samples/examples.fasta';  
  var matchScore = 1;
  var misMatchScore = -1;
  var gapScore = -1;
  
  smithW.alignFile(inputFile, matchScore, misMatchScore, gapScore, function(err,data){
      if(err){
          console.log(err);
      }else{
          console.log(data);
      }
  });

Align sequence file and output pairwise alignment along with score matrix

.alignFileGetMatrix (inputFile, matchScore, misMatchScore, gapScore, callback) callback passed (err, data)

NOTE: You can build the bundled binary executable by running,

node util/psaToolBuilder.js