This figure is created with the following script:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Bio::Graphics;
use Bio::SeqFeature::Generic;
use List::Compare;
use List::Util qw(max);

my %nofseq = ( 0 => 300, 1 => 300, 2 => 300, 3 => 300, 4 => 300, 5 => 
+300 );
my @seqid = keys %nofseq;
my @lenlist = values %nofseq; #Sequence length
my $maxlen = max (@lenlist);
#print Dumper \@seqid ;

my $panel = Bio::Graphics::Panel->new(
    -length    => 300,
    -width     => 500,
    -pad_left  => 70,
    -pad_right => 70,
    -key_style => 'left',
    -connector => 'solid',
);

my $flen = Bio::SeqFeature::Generic->new( 
        -start => 1,
        -end => 300, 
);

    my $track1 = $panel->add_track(
        $flen,
        -glyph   => 'arrow',
        -tick    => 2,
        -fgcolor => 'black',
        -double  => 1,
    );



my %nlist;

while ( <DATA> ) {
    chomp;
    next if /^\#/;
    my ($sqi,$pos,$str,$progname) = split /\,/;
    my $start = $pos + $nofseq{$sqi};
    my $end = $start + length($str) + 1;
    push @{$nlist{$sqi}}, $start." ".$end." ".$progname;
}               

# Check which sequence has no motifs;
my @bssi = keys %nlist;

my $lc = List::Compare->new(\@seqid, \@bssi);
my @comp = $lc->get_unique;


foreach my $comp ( @comp  ) {
    push @{$nlist{$comp}}, '0'." ".'0'." "."NONE";

}               

my %prog_color = ( "WEEDER" => 3000, "MEME" => 200, "NONE" => 0 );

foreach my $seqid ( sort keys %nlist ) {


    my $track = $panel->add_track(
        -glyph     => 'graded_segments',
        -key       => "SEQ ". $seqid,
        -connector => "solid"
        -label     => 1,
        -bgcolor   => 'blue',
        -bump      =>  +1,
        -height    =>  8,
        -min_score => 0,
        -max_score => 5000
    );


    foreach my $range ( @{$nlist{$seqid}} ) {

        my ($st,$en,$progname) = split(" ", $range);
        my $dname = " ";
        if ( $st != 0 and $en !=0  ) {
           $dname = "Seq ". $seqid;
        }

        my $score;
        if ( $progname eq "WEEDER" ) {
            $score = $prog_color{$progname};

        }
        elsif ($progname eq "MEME" ) {
            $score = $prog_color{$progname};
        }
        
        my $feature = Bio::SeqFeature::Generic->new(
            -display_name => $dname,
            -start        => $st,
            -end          => $en,
            -score        => $score
        );

        $track->add_feature($feature);

    }

}

print $panel->png;


__DATA__
# sequence number,pos,binding sites,program
4,-63,AGCTTTCTCT,MEME
0,-22,AACTTTGTAC,WEEDER
1,-13,AAGTTTCTCT,WEEDER
5,-228,ACCTTTGCCA,MEME
5,-121,AAGTTTGTCT,WEEDER
5,-88,AAGTTTTTCC,SPACE
3,-148,AACTTAGTCA,MEME
0,-184,AACTTTGTCT,MEME
[download]

The DATA is simply just list of string and its location in their respective sequence. The figure is just the plot of it out.

As you can see from the figure, there are some misgivings of my script above.

• The arrow track need to be represented in negative form. I.e. instead of 1 to 300, we use -300 to 0. I tried this, but won't do:

  my $flen = Bio::SeqFeature::Generic->new(
         -start => -300,
         -end => 0, );
  [download]

• And how can I make these number to appear for every gridpoints (not just two as I have now).
• The "connector" doesn't seem to work.
• It needs a LEGEND to describe the color of each block (WEEDER = purple, MEME=white).

I was thinking to mimic this figure.
Does anybody has experience in dealing with such issues with Bio::Graphics? Any idea how to achieve that?

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