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Needleman-Wunsch Alignment in PHP
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ABOUT

An implementation of the Needleman-Wunsch global alignment algorithm in PHP.
Computes the alignment scoring table and optimal global alignment. Provides
methods to render output in both HTML for display in a web browser and ASCII
for printing to a terminal. 

USAGE

This code was written for educational purposes to demonstrate how the algorithm
works. It is not intended for use in real sequence alignment or use with very
large sequences. Example usage:
 
  <?php

  require_once('needleman-wunsch-class.php');

  $nw = new NeedlemanWunsch(1, 0, -1);
  $seq1 = 'ACAGTCGAACG';
  $seq2 = 'ACCGTCCG';

  $nw->renderAsASCII($seq1, $seq2);

  ?>

For a complete interactive example see: alignment.php

Example output:

Alignment Score Table

                   A       C       C       G       T       C       C       G
           0      -1      -2      -3      -4      -5      -6      -7      -8
A         -1    ↖  1*   ←  0    ← -1    ← -2    ← -3    ← -4    ← -5    ← -6
C         -2    ↑  0    ↖  2*   ←  1    ←  0    ← -1    ← -2    ← -3    ← -4
A         -3    ↑ -1    ↑  1    ↖  2*   ←  1    ←  0    ← -1    ← -2    ← -3
G         -4    ↑ -2    ↑  0    ↑  1    ↖  3*   ←  2    ←  1    ←  0    ← -1
T         -5    ↑ -3    ↑ -1    ↑  0    ↑  2    ↖  4*   ←  3    ←  2    ←  1
C         -6    ↑ -4    ↑ -2    ↖  0    ↑  1    ↑  3    ↖  5*   ←  4    ←  3
G         -7    ↑ -5    ↑ -3    ↑ -1    ↖  1    ↑  2    ↑  4*   ↖  5    ↖  5
A         -8    ↑ -6    ↑ -4    ↑ -2    ↑  0    ↑  1    ↑  3*   ↑  4    ↖  5
A         -9    ↑ -7    ↑ -5    ↑ -3    ↑ -1    ↑  0    ↑  2*   ↑  3    ↑  4
C         -10   ↑ -8    ↑ -6    ↑ -4    ↑ -2    ↑ -1    ↑  1    ↖  3*   ↑  3
G         -11   ↑ -9    ↑ -7    ↑ -5    ↑ -3    ↑ -2    ↑  0    ↑  2    ↖  4*

Optimal Global Alignment (score = 4)
A C C G T C - - - C G
| |   | | |       | |
A C A G T C G A A C G


AUTHOR

Andrew E. Bruno <aeb@qnot.org>


REFERENCES

[1] https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm