[GENERAL]
description = Volvox Example Database
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/usr/local/apache/doc/gbrowse/databases/volvox'
plugins = Aligner RestrictionAnnotator GFFDumper
drag and drop = 1
balloon tips = 1
titles are balloons = 1
# list of tracks to turn on by default
default features = ExampleFeatures
# examples to show in the introduction
examples = ctgA
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
# feature to show on startup
initial landmark = ctgA:1..10000
# max and default segment sizes for detailed view
max segment = 50000
default segment = 5000
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 50000
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
label density = 25
bump density = 100
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Gene Protein
# other customization options...
# HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS
# inside the section
head =
# at the top...
header =
# a footer
footer =
$Id: volvox_final.conf,v 1.6.6.2.2.4.2.1 2008/03/26 13:36:37 lstein Exp $
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'
########################
# 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 = remark
glyph = generic
stranded = 1
bgcolor = orange
height = 10
key = Example Features
[NameTest]
feature = protein_coding_primary_transcript polypeptide
glyph = generic
stranded = 1
bgcolor = green
height = 10
key = Name test track
[Motifs]
feature = polypeptide_domain
glyph = span
height = 5
description = 1
balloon hover = Gene $name
balloon click = Gene $name
Search Google
Search NCBI
key = Example motifs
[Alignments]
feature = match
glyph = segments
category = Alignments
key = Example alignments
[Genes]
feature = gene
glyph = gene
bgcolor = peachpuff
label_transcripts = 1
draw_translation = 1
category = Genes
key = Protein-coding genes
[ReadingFrame]
feature = mRNA
glyph = cds
ignore_empty_phase = 1
category = Genes
key = Frame usage
[CDS]
feature = CDS:predicted mRNA:exonerate
glyph = gene
bgcolor = white
category = Genes
key = Predicted genes
[Transcript]
feature = mRNA:exonerate
glyph = so_transcript
description = 1
bgcolor = beige
category = Genes
key = Exonerate predictions
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
connector = dashed
strand_arrow = 1
description = 1
key = Fingerprinted BACs
[TransChip1]
feature = microarray_oligo
glyph = wiggle_density
#glyph = wiggle_xyplot
#graph_type = linepoints
#point_symbol = disc
#point_radius = 3
height = 30
bgcolor = blue
category = Genes
description = 1
key = Transcriptional Profile
[TransChip2]
feature = microarray_oligo
glyph = wiggle_xyplot
#graph_type = linepoints
#point_symbol = disc
#point_radius = 3
height = 30
bgcolor = blue
category = Genes
description = 1
key = Transcriptional Profile
[DNA]
glyph = dna
global feature = 1
height = 40
do_gc = 1
gc_window = auto
fgcolor = red
axis_color = blue
strand = both
key = DNA/GC Content
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
start_codons = 0
stop_codons = 1
translation = 6frame
key = 6-frame translation
[EST]
feature = EST_match:est
height = 6
glyph = segments
draw_target = 1
show_mismatch = 1
canonical_strand = 1
bgcolor = sub {
my $feature = shift;
my $name = $feature->display_name;
if ($name =~ /\.5$/) {
return 'red';
} else {
return 'orange';
}
}
group_pattern = /\.[53]$/
key = ESTs
[Traces]
feature = read
glyph = trace
fgcolor = black
bgcolor = orange
strand_arrow = 1
height = 6
description = 1
a_color = green
c_color = blue
g_color = black
t_color = red
trace_height = 80
trace_prefix = http://localhost/gbrowse/tutorial/data_files/
key = Traces
########################
# Plugin configuration
########################
[Aligner:plugin]
alignable_tracks = EST
upcase_tracks = CDS Motifs
upcase_default = CDS
[Motifs:overview]
feature = polypeptide_domain
glyph = span
height = 5
description = 1
label = 1
key = Motifs