my %value = (
  G => 0,
  A => 1,
  T => 2,
  C => 3,
);

##</code><code>##

$number = $w[$n]*(4**$n) + $w[$n-1]*(4**($n-1)) + ... + $w[0]

##</code><code>##

sub word_to_number {
  my (@w) = @_;
  my $res = 0;
  while (@w) {
    $res = $res * 4;
    $res += $value{ pop @w };
  };
};

##</code><code>##

open my $frequencies, ">+", 'frequencies.bin'
  or die "$!";
binmode $frequencies;

...

while (words_are_available()) {
  my @word = split //, get_next_word();
  my $offset = word_to_number(@word);

  seek $frequencies, $offset * 4;
  read $frequencies, my $old_count, 4;
  $old_count = unpack "N", $old_count;
  my $count = $old_count + 1;
  seek $requencies, $offset * 4;
  write $frequencies, pack "N", $count;
};