needleman-wrapper v1.0.0

needleman-wrapper

A simple node module that wraps the functionalities of a needleman-wunsch implementation written in C

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

Install

You can install needleman-wrapper by running,

npm install needleman-wrapper

Usage

Align two unaligned sequences

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

  const needleman = require('needleman-wrapper');
  var sequence1 = 'AADBFGTRHYSRRFDERS';
  var sequence2 = 'AADGTDRSYSRFFDERTS';
  var matchScore = 1;
  var misMatchScore = -1;
  var gapScore = -1;
  
  needleman.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

• .alignPairGetScore (sequence1, sequence2, matchScore, misMatchScore, gapScore, callback) callback passed (err, 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 needleman = require('needleman-wrapper');
    var inputFile = 'samples/examples.fasta';  
    var matchScore = 1;
    var misMatchScore = -1;
    var gapScore = -1;
    
    needleman.alignFile(inputFile, matchScore, misMatchScore, gapScore, function(err,data){
        if(err){
            console.log(err);
        }else{
            console.log(data);
        }
    });

Align sequence file and output alignments along with score

• .alignFileGetScore (inputFile, matchScore, misMatchScore, gapScore, callback) callback passed (err, 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