# note: for this configuration to work, you will need to launch gbrowse slave
# servers on ports 8100 & 8101 on localhost.
[GENERAL]
description = Volvox Example Database
database = volvox1
aggregators = match
BAC{left_end_read,right_end_read/BAC}
processed_transcript
coding
tprofile{tlevel}
qtl{signal/peak}
chromosome{chromosome_band,centromere/contig}
plugins = Aligner RestrictionAnnotator ProteinDumper TestFinder
initial landmark = ctgA:1..10000
# the extra left padding makes it easier to see the mRNA labels,
# which are printed on the left by the new "gene" glyph
pad_left = 60
pad_right = 30
# list of tracks to turn on by default
default features = ExampleFeatures
Motifs:overview
TransChip:region
Transcripts
Transcripts:overview
reference class = Contig
# examples to show in the introduction
examples = ctgA
# "automatic" classes to try when an unqualified identifier is given
automatic classes = My_feature Motif Binding_site Match
show track categories = 0
### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
html2 = This is overridden
# max and default segment sizes for detailed view
max segment = 100000
default segment = 5000
# size of the "region panel"
region segment = 20000
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 50000 75000 100000
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
default varying = 1
# DAS reference server
das mapmaster = SELF
########################
# Named databases
########################
[volvox1:database]
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-dsn $ENV{GBROWSE_DOCS}/databases/volvox/
[volvox2:database]
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-gff $ENV{GBROWSE_DOCS}/databases/volvox2
[volvox3:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dsn $ENV{GBROWSE_DOCS}/databases/volvox3
[volvox4:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dsn $ENV{GBROWSE_DOCS}/databases/volvox4
########################
# Plugin configuration
########################
[Aligner:plugin]
alignable_tracks = EST
upcase_tracks = CDS Motifs
upcase_default = CDS
########################
# Default glyph settings
########################
[TRACK DEFAULTS]
glyph = generic
height = 10
bgcolor = lightgrey
fgcolor = black
font2color = blue
label density = 25
bump density = 100
# where to link to when user clicks in detailed view
link = AUTO
################## TRACK CONFIGURATION ####################
# the remainder of the sections configure individual tracks
###########################################################
[ExampleFeatures]
feature = my_feature
glyph = generic
stranded = 1
bgcolor = blue
height = 10
category = Genes
das category = example
citation = These are undifferentiated features that are displayed using the generic glyph
with a bgcolor of blue.
key = Example features
[Motifs]
feature = motif
glyph = span
height = 5
description = 1
das category = example
category = Proteins
key = Example motifs
[Clones]
feature = BAC
glyph = segments_new
bgcolor = yellow
strand_arrow = 1
description = 1
das category = example
category = Alignments
key = Fingerprinted BACs
[Transcripts]
feature = processed_transcript gene
glyph = processed_transcript
bgcolor = peachpuff
category = Genes
key = Protein-coding genes
[Transcripts:overview]
feature = processed_transcript gene
glyph = processed_transcript
bgcolor = peachpuff
height = 12
category = Genes
key = Protein-coding genes
[CDS]
feature = coding
glyph = cds
category = Genes
phase_style = 012
translation = 3frame
key = Frame usage
[Variation]
feature = variation
glyph = triangle
point = 1
orient = N
description = 1
restrict = Order deny,allow
deny from all
allow from .cshl.edu .ebi.ed.uk
require valid-user
key = Variations
[DNA]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
strand = both
category = Genes
link = ''
key = DNA/GC Content
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
start_codons = 0
stop_codons = 1
codontable = 2
category = Proteins
translation = 6frame
key = 6-frame translation
[Translation:30000]
hide = 1
[Motifs:overview]
feature = motif
glyph = span
height = 5
description = 0
label = 1
key = Motifs
[motif:details]
translation = sub {
my $value = shift;
$value =~ s/(\S{1,60})/$1\n/g;
"<pre>$value</pre>";
}
Note = <a href="http://www.google.com/search?q=$value">$value</a>
[ProteinDumper:plugin]
geneticcode=12
[BindingSites]
database = volvox2
feature = binding_site
key = Binding Sites
[builtin:karyotype]
chromosome = chromosome
chrom_height = 120
chrom_width = 16
fgcolor = black
bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray
gpos75:darkgray gpos100:black gvar:var stalk:#666666
arcradius = 7
key = You should never see this
[CleavageSites]
database = volvox3
feature = cleavage_site
key = Cleavage Sites
[Alignments]
database = volvox2
remote renderer = http://localhost:8100
feature = match
glyph = segments
category = Alignments
das category = example
key = Example alignments
[Alignments:30000]
glyph = box
[Alignments:45000]
glyph = box
label = 0
bump = 0
[EST]
database = volvox4
remote renderer = http://localhost:8101
feature = EST_match
glyph = segments
height = 8
draw_target = 1
true_target = 0
label_position = left
# draw_dna = 1
show_mismatch = 1
realign = 1
canonical_strand = 1
bgcolor = sub {
my $feature = shift;
my $name = $feature->display_name;
if ($name =~ /\.5$/) {
return 'red';
} else {
return 'orange';
}
}
box_subparts = 0
group_pattern = /\.[53]$/
category = Alignments
key = ESTs
[EST:200]
label_position = top
# this one uses a slave renderer
[TransChip]
database = volvox2
feature = tprofile
remote renderer = http://localhost:8100
glyph = xyplot
graph_type = boxes
height = 50
bgcolor = orange
min_score = 0
max_score = 1000
scale = right
category = Genes
key = Transcriptional Profile
# this one uses the main renderer
[TransChip:region]
database = volvox2
feature = tprofile
glyph = xyplot
graph_type = boxes
height = 50
min_score = 0
max_score = 1000
bgcolor = blue
scale = right
key = Profile