[GENERAL]
description = Volvox Example Database
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-gff '/usr/local/apache/doc/gbrowse/databases/volvox'
aggregators = match
BAC{left_end_read,right_end_read/BAC}
processed_transcript
coding
plugins =
# list of tracks to turn on by default
default features = ExampleFeatures
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
### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the section
head =
# at the top...
header =
# a footer
footer =
$Id: volvox3.conf,v 1.1.2.1 2008/03/11 14:31:28 lstein Exp $
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
# 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
# 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
########################
# 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
key = Example features
[Motifs]
feature = motif
glyph = span
height = 5
description = 1
key = Example motifs
[Alignments]
feature = match
glyph = segments
key = Example alignments
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
strand_arrow = 1
description = 1
key = Fingerprinted BACs
[Transcripts]
feature = processed_transcript gene
glyph = processed_transcript
bgcolor = peachpuff
description = 1
key = Protein-coding genes
[CDS]
feature = coding
glyph = cds
key = Frame usage