[GENERAL]
description = Volvox Example Database
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-dir '/usr/local/apache/doc/gbrowse/databases/volvox'
aggregators = match
BAC{left_end_read,right_end_read/BAC}
processed_transcript
coding
tprofile{tlevel}
plugins = Aligner RestrictionAnnotator
# list of tracks to turn on by default
default features = ExampleFeatures
Motifs:overview
TransChip:region
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: volvox_final_withPhylo.conf,v 1.1 2008-10-22 18:54:40 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
# size of the "region panel"
region segment = 20000
# 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
########################
# 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 = Examples
key = Example features
[Motifs]
feature = motif
glyph = span
height = 5
description = 1
category = Proteins
key = Example motifs
[Alignments]
feature = match
glyph = segments
category = Alignments
key = Example alignments
[Alignments:30000]
glyph = box
label = 0
[Alignments:45000]
glyph = box
bump = 0
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
strand_arrow = 1
description = 1
category = Alignments
key = Fingerprinted BACs
[Transcripts]
feature = processed_transcript gene
glyph = processed_transcript
bgcolor = peachpuff
description = 1
category = Genes
key = Protein-coding genes
[CDS]
feature = coding
glyph = cds
category = Genes
key = Frame usage
[EST]
feature = match:est
glyph = segments
height = 6
draw_target = 1
show_mismatch = 1
canonical_strand = 1
bgcolor = sub {
my $feature = shift;
my $name = $feature->display_name;
if ($name =~ /\.5$/) {
return 'red';
} else {
return 'orange';
}
}
group_pattern = /\.[53]$/
category = Alignments
key = ESTs
[TransChip]
feature = tprofile
glyph = xyplot
graph_type = boxes
height = 50
min_score = 0
max_score = 1000
scale = right
category = Genes
key = Transcriptional Profile
[TransChip:region]
feature = tprofile
glyph = xyplot
graph_type = boxes
height = 50
min_score = 0
max_score = 1000
bgcolor = blue
scale = right
key = Profile
[DNA]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
strand = both
category = Examples
key = DNA/GC Content
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
start_codons = 0
stop_codons = 1
category = Proteins
translation = 6frame
key = 6-frame translation
[Motifs:overview]
feature = motif
glyph = span
height = 5
description = 0
label = 1
key = Motifs
[Traces]
feature = trace
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
show_border = 1
[PhyloAlignment]
glyph = phylo_align
global feature = 1
height = 40
draw_clado_left = 0
species_spacing = 1.2
species_spacing_score = 5
hide_label = 0
fgcolor = darkblue
errcolor = red
axis_color = darkorange
mid_axis_color = yellow
clado_bg = peachpuff
bg_color = white
targ_color = yellowgreen
ref_color = palegoldenrod
key = Phylogenetic Alignment
reference = volvox
#tree_step_width = 5
tree_file = /Users/mokada/development/gsoc/head/htdocs/gbrowse/databases/volvox/species.tre
tree_format = newick