use Bio::AlignIO;
  # read in an alignment from meme
  my $in = Bio::AlignIO->new(-format => 'meme',
                             -file   => 'meme.out');
  while( my $aln = $in->next_aln ) {
     # do something with the alignment
  }

	my ($self) = @_;
	my $aln = Bio::SimpleAlign->new(-source => 'meme');
	my $line;
	my $good_align_sec = 0;
	my $in_align_sec = 0;
	while (!$good_align_sec && defined($line = $self->_readline())) {
		if (!$in_align_sec) {
			# Check for the meme header
			if ($line =~ /^\s*MEME\s+version\s+(\S+)/ ){
				$self->{'meme_vers'} = $1;
                my ($vers) = $self->{'meme_vers'} =~ /^(\d)/;
				$self->throw($MEME_VERS_ERR) unless ($vers >= 3);
				$self->{'seen_header'} = 1;
	      }
			# Check if they've output the HTML version
			if ($line =~ /\<TITLE\>/i){
				$self->throw($HTML_VERS_ERR);
	      }
			# Check if we're going into an alignment section
			if ($line =~ /sites sorted by position/) {
				$self->throw($MEME_NO_HEADER_ERR) unless ($self->{'seen_header'});
				$in_align_sec = 1;
			}
		} elsif ($line =~ /^(\S+)\s+([+-]?)\s+(\d+)\s+
                       (\S+)\s+([.ACTGX\-]*)\s+([ACTGX\-]+)\s+
                       ([.ACTGX\-]*)/xi ) {
			# Got a sequence line
			my $seq_name = $1;
			my $strand = ($2 eq '-') ? -1 : 1;
			my $start_pos = $3;
			my $central = uc($6);

			# my $p_val = $4;
			# my $left_flank = uc($5);
			# my $right_flank = uc($7);

			# Info about the flanking sequence
			# my $start_len = ($strand > 0) ? length($left_flank) :
			# length($right_flank);
			# my $end_len = ($strand > 0) ? length($right_flank) :
			# length($left_flank);

			# Make the sequence.  Meme gives the start coordinate at the left
			# hand side of the motif relative to the INPUT sequence.
			my $end_pos = $start_pos + length($central) - 1;
			my $seq = new Bio::LocatableSeq(-seq    => $central,
													  -id     => $seq_name,
													  -start  => $start_pos,
													  -end    => $end_pos,
													  -strand => $strand
													 );
			# Add the sequence motif to the alignment
			$aln->add_seq($seq);
		} elsif (($line =~ /^\-/) || ($line =~ /Sequence name/)){
			# These are acceptable things to be in the site section
		} elsif ($line =~ /^\s*$/){
			# This ends the site section
			$in_align_sec = 0;
			$good_align_sec = 1;
		} else{
			$self->warn("Unrecognized format:\n$line");
			return 0;
		}

   my ($self,@aln) = @_;
   $self->throw_not_implemented();

  my($self,@args) = @_;

  # Call into our base version
  $self->SUPER::_initialize(@args);

  # Then initialize our data variables
  $self->{'seen_header'} = 0;

  http://bugzilla.open-bio.org/

 Bbased on the Bio::SeqIO modules by Ewan Birney and others
 Email: benb@fruitfly.berkeley.edu