I'm not 100% sure what you want to do here Jeri. The sample below assumes you have a single string composed of 9 character sequences. When the 'for' has run the keys of %uniq will be the unique 9 character sequences.

It would take a while and a lot of memory over 5 mill x 9 char sequences!

my $str = join '',(648040620,637132715,649986572,648040620 );

my $proteins_count = length ($str)/9;

my %uniq;

do { $uniq{$_}++ unless $uniq{$_} } 
 for unpack "(A9)$proteins_count" , $str;

print "@{[keys %uniq]}\n";
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Prints ..
637132715 648040620 649986572