"doesn't work" isn't an error report. You'll have to provide more information when asking for help. See How do I post a question effectively? and PerlMonks for the Absolute Beginner.

Although marto is quite right, perhaps I can make an educated guess here?

The code as given by snape is incomplete. When I add this before the code:

#! perl
use strict;
use warnings;

my $MATCH    =  1;
my $MISMATCH = -1;
my $GAP      = -1;

chomp(my $seq1 = <DATA>);
chomp(my $seq2 = <DATA>);
[download]

and this after the code:

__DATA__
ATGTAGACCTAGATCATGATGACTGATGAT
ATTACCGATGACTGATGACTGATGACTGAT
[download]

I get the same output as reported by snape.

Disclaimer: I have no knowledge of the Needleman Wunsch algorithm (if that’s what this code is implementing), nor of what it’s for. :-)

Hope that helps,