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;
};