while (!eof(DATFILE))
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---

sub _read {
   my ($fh, $bytes_to_read) = @_;

   my $buf = '';
   while ($bytes_to_read) {
      my $bytes_read = read($fh, $buf, $bytes_to_read, length($buf));
      if (!$bytes_read) {
         die "Error reading: $!\n" if !defined($bytes_read);
         die "Unexpected EOF\n";
      }

      $size -= $bytes_read;
   }

   return $buf;
}

sub read_uint32  { my ($fh) = @_; unpack('N', _read($fh, 4)) }  #Or V?
sub read_uint16  { my ($fh) = @_; unpack('n', _read($fh, 2)) }  #Or v?
sub read_pstring { my ($fh) = @_; _read($fh, read_uint16($fh)) }

{
   open(my $fh, '<:raw', $datfilename) or die $!;
   read_uint32($fh);
   while (!eof($fh)) {
      my $profile_id = read_uint32($fh);
      my $seq1 = read_pstring($fh);
      my $seq2 = read_pstring($fh);
      read_uint16($fh);

      ...
   }
}
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Or if the "trailing zero" is meant to indicate the end of a list of sequences,

{
   open(my $fh, '<:raw', $datfilename) or die $!;
   read_uint32($fh);
   while (!eof($fh)) {
      my $profile_id = read_uint32($fh);
      my @seqs;
      while (length( my $seq = read_pstring($fh) )) {
         push @seqs, $seq;
      }

      ...
   }
}
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