[GENERAL]
description = Volvox Example Database
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/usr/local/apache/doc/gbrowse/databases/volvox'
plugins =
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: volvox3.conf,v 1.6.8.1.2.3 2008/08/22 17:39:40 scottcain 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 = blue
height = 10
key = Example Features
[Motifs]
feature = polypeptide_domain
glyph = span
height = 5
description = 1
key = Example motifs
[Alignments]
feature = match
glyph = segments
key = Example alignments
[Genes]
feature = gene
glyph = gene
bgcolor = peachpuff
label_transcripts = 1
draw_translation = 1
category = Genes
key = Protein-coding genes
[Transcripts]
feature = processed_transcript gene
glyph = processed_transcript
height = 8
bgcolor = black
utr_color = black
thin_utr = 1
decorate_introns = 1
description = 1
key = Protein-coding genes
[CDS]
feature = CDS:predicted
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
[ReadingFrame]
feature = mRNA
glyph = cds
ignore_empty_phase = 1
category = Genes
key = Frame usage
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
connector = dashed
strand_arrow = 1
description = 1
key = Fingerprinted BACs