[GENERAL]
description = BioSQL - 1 Mbp of chr 2 of Arabidopsis
db_adaptor = Bio::DB::Das::BioSQL
db_args = driver mysql
dbname bioperl
namespace arabidopsis
version 3
host hostname
user username
pass password
port 3306
plugins = SequenceDumper FastaDumper RestrictionAnnotator
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
# Default glyph settings
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
label density = 25
bump density = 100
# where to link to when user clicks in detaild view
link = http://localhost/perl/gbrowse?ref=$ref;start=$start;stop=$end
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
default features = CDS
Genes
#repeat_region
# max and default segment sizes for detailed view
max segment = 500000
default segment = 50000
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
low res = 200000
# colors of the overview, detailed map and key
overview bgcolor = wheat
detailed bgcolor = white
key bgcolor = beige
footer = <hr>
<table width="100%">
<TR>
<TD align="LEFT" class="databody">
For the source code for this browser, see the <a href="http://www.gmod.org">
Generic Model Organism Database Project.</a> For other questions, send
mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
</TD>
</TR>
</table>
<hr>
<pre>$Id: 06.biosql.conf,v 1.4 2005-12-09 22:19:09 mwz444 Exp $</pre>
# examples to show in the introduction
examples = AP000868
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Accession
init_code = *Bio::SeqFeature::Generic::type = \&Bio::SeqFeature::Generic::primary_tag;
# the remainder of the sections configure particular features to show
[CDS]
feature = CDS
glyph = transcript2
#glyph = generic
bgcolor = turquoise
fgcolor = black
height = 10
connector = solid
label = sub {
my $feature = shift;
my @notes;
if ($feature->primary_tag eq "CDS")
{
foreach (qw(product gene)) {
next unless $feature->has_tag($_);
@notes = $feature->each_tag_value($_);
last;
}
return $notes[0];
}
else
{
return $feature->display_name;
}
}
description = sub {
my $feature = shift;
my @notes;
if ($feature->primary_tag eq "CDS")
{
foreach (qw(note)) {
next unless $feature->has_tag($_);
@notes = $feature->each_tag_value($_);
last;
}
return unless @notes;
substr($notes[0],30) = '...' if length $notes[0] > 30;
return $notes[0];
}
else
{
my $description;
foreach ($feature->all_tags) {
my @values = $feature->each_tag_value($_);
$description .= $_ eq 'note' ? "@values" : "$_=@values; ";
}
$description =~ s/; $//; # get rid of last
return $description;
}
}
# key = Predicted transcripts
[REPEAT]
feature = repeat_region
glyph = generic
bgcolor = red
height = 10
description = 1
key = Repeat regionss
[TranslationF]
glyph = translation
global feature = 1
frame0 = cadetblue
frame1 = blue
frame2 = darkblue
height = 20
fgcolor = purple
strand = +1
translation = 3frame
key = 3-frame translation (forward)
[DNA/GC Content]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
[TranslationR]
glyph = translation
global feature = 1
frame0 = darkred
frame1 = red
frame2 = crimson
height = 20
fgcolor = blue
strand = -1
translation = 3frame
key = 3-frame translation (reverse)
[Genes]
feature = gene:sgd
glyph = generic
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height = 6
description = 1
key = Named gene