Align::NW - Needleman-Wunsch algorithm for optimal global sequence alignment


    use Align::NW;
    $payoff = { match      => $match,
		mismatch   => $mismatch,
		gap_open   => $gap_open,
		gap_extend => $gap_extend };
    $nw = new Align::NW $a, $b, $payoff, %options
    $score = $nw->get_score;
    $align = $nw->get_align;


Align::NW finds the optimal global alignment of the sequences $a and $b, subject to the $payoff matrix.


Align::NW uses the Needleman-Wunsch dynamic programming algorithm. This algorithm runs in O(a*b*(a+b)), where a and b are the lengths of the two sequences to be aligned.


An alignment of two sequences is represented by three lines. The first line shows the first sequence, and the third line shows the second sequence.

The second line has a row of symbols. The symbol is a vertical bar where ever characters in the two sequences match, and a space where ever they do not.

Dots may be inserted in either sequence to represent gaps.

For example, the two sequences


could be aligned like this

    || |   | || 

As shown, there are 6 matches, 2 mismatches, and one gap of length 3.

Align::NW retuns an alignment as a hash

    $align = { a => $a,
	       s => $s,
	       b => $b };

$a and $b are the two sequences. $s is the line of symbols.

The Payoff Matrix

The alignment is scored according to a payoff matrix

    $payoff = { match      => $match,
		mismatch   => $mismatch,
		gap_open   => $gap_open,
		gap_extend => $gap_extend };

The entries in the matrix are the number of points added to the score

For correct operation, match must be positive, and the other entries must be negative.


Given the payoff matrix

   $payoff = { match      =>  4,
	       mismatch   => -3,
	       gap_open   => -2,
	       gap_extend => -1 };

The sequences


are aligned and scored like this

                a b c d e f g h a j k l m
                | |   |       |   | | 
                a b b d . . . h i j k
    match       4 4   4       4   4 4  
    mismatch       -3          -3
    gap_open           -2
    gap_extend         -1-1-1

for a total score of 24-6-2-3 = 15. The algorithm guarantees that no other alignment of these two sequences has a higher score under this payoff matrix.


$nw = new Align::NW $a, $b, $payoff, %options
Creates and returns a new Align::NW object. $a and $b are the sequences to be aligned. $payoff is the payoff matrix, described above. Additional options maybe passed in the %options hash; see /OPTIONS for details.
Fills in the score matrix for $nw. This is the O(a*b*(a+b)) operation.
Backtracks through the score matrix and generates an alignment for the two sequences. score must be called before align.
$score = $nw->get_score
Returns the score of the alignment. score must be called before get_score.
$align = $nw->get_align
Returns the alignment of the two sequences, as described above in /Alignments. align must be called before get_align.
Pretty prints the alignment to STDOUT. align must be called before print_align.
Dumps the score matrix to STDOUT. This is useful mainly for debugging. The matrix is not pretty printed; line wrapping makes large matrices difficult to read.


Options may be passed to new in the %options hash. The following options are defined.

Verbose output. Prints some dots to STDERR. Useful for monitoring the progress of large alignments.


There are usually some some tutorials on Needleman-Wunsch and Smith-Waterman alignment floating around on the web. I used to provide links to some, but they kept going 404. If you Google around a bit you can probably find a current one.



Steven W. McDougall <>


Copyright 1999-2003 by Steven W. McDougall. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.