Things you can try: use bigint (see bigint), and use ordinary print instead of printf() for debugging.

Finally your hash access is unnecessary complicated - instead of the grep you can just access $iupac_dgn{$residues} directly.

The simplified code looks like this:

#!/usr/bin/perl
use strict;
use warnings;
use integer;

my %iupac_dgn;
my @iupac_code = ('M','R','W','S','Y','K','V','H','D','B','N');
my @iupac_den = ('2','2','2','2','2','2','3','3','3','3','4');     
@iupac_dgn{@iupac_code}=@iupac_den;

my $string = 'GGNMDNNSNNNNDBNVWVSMNNHYNBNG'; 
my @residues = split(//, $string);
my $degeneracy = 1;

foreach my $residues(@residues){
    $degeneracy *= $iupac_dgn{$residues} || 1;
}

printf "%28s, %30s\n", $string, $degeneracy;
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If you are on a 32-bit system, you must use Math::BigInt. The following returns 2348273369088.

#!/usr/bin/perl
use strict;
use warnings;
use integer;
use Math::BigInt;

my %iupac_dgn;
my @iupac_code = ('M','R','W','S','Y','K','V','H','D','B','N');
my @iupac_den = ('2','2','2','2','2','2','3','3','3','3','4');     
@iupac_dgn{@iupac_code}=@iupac_den;

my $string = 'GGNMDNNSNNNNDBNVWVSMNNHYNBNG'; 
my @residues = split(//, $string);
my $degeneracy = Math::BigInt->new( 1 );

foreach my $residues(@residues){
    $degeneracy *= $iupac_dgn{$residues} || 1;
}

printf "%28s, %30s\n", $string, $degeneracy;
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Update: I will concur with Tye as long as the result is less than 2 ** 49 on a 32b machine/implementation. Thanks.

Good Luck. -c

If you are on a 32-bit system, you must use Math::BigInt.

Don't be foolish. :) Just don't use the stupid integer.pm module:

#!/usr/bin/perl
use strict;
use warnings;
# use integer;

my %iupac_dgn;
my @iupac_code=('M','R','W','S','Y','K','V','H','D','B','N');
my @iupac_den=('2','2','2','2','2','2','3','3','3','3','4');
@iupac_dgn{@iupac_code}=@iupac_den;

my $string = 'GGNMDNNSNNNNDBNVWVSMNNHYNBNG';
my @residues = split( //, $string );
my $degeneracy = 1;

foreach my $residues(  @residues  ) {
    if(  grep( m/^$residues$/, keys %iupac_dgn )  ) {
        my $factor = $iupac_dgn{$residues};
        $degeneracy = ($factor * $degeneracy);
    }
}

printf "%28s, %30d", $string, $degeneracy;
__END__
GGNMDNNSNNNNDBNVWVSMNNHYNBNG,                  2348273369088
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- tye        

You apparently have a perl binary that only supports 32-bit integers.  And the value you compute (2348273369088) is much larger than 32 bits can hold. Represented as binary, it is:

   10_00100010_11000000_00000000_00000000_00000000
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So, it gets truncated

               11000000_00000000_00000000_00000000
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and as the leftmost (most significant) bit happens to be 1, and you used %d (= signed int) in printf, it is interpreted as a negative value (see Two's Complement). Effectively the same as

printf "%d", 0b11000000_00000000_00000000_00000000 - 2**32;    # -1073
+741824
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with a perl that supports ints larger than 32 bit.