Ah, I did it using the following code:

my @array_q3=(); #create the array to store all words in the file
open INFILE3, "<file";
while( my $line3 = <INFILE3>)  
{   
    chomp $line3;
    push @array_q3, $line3;    
}
close INFILE3;

#sort the array so we can identify the duplicates
my @sorted_array_q3 = sort(@array_q3);
my @unique_array;

#iterate through the sorted array and check for unique elements
foreach my $element ( @sorted_array_q3 )
{
  if ( ! grep( /$element/, @unique_array ) )
  {
     push( @unique_array, $element );
  }
}

#print the unique elements in the file clean.acc\n";
open OUTFILE3, ">unique_codes";
for (my $m=0; $m<=$#unique_array; $m++)
{
  print OUTFILE3 $unique_array[$m]."\n";
}
close OUTFILE3;
[download]

My problem here is with grep, since I seem to miss one element... The element has the code J00148 and apparently there is a conflict with another element, namely AJ001487.
What must I add in my grep conditional?