[GENERAL]
description = Volvox Mysql Database (GFF3)
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=volvoxgff3
# aggregators are ignored in GFF3 files
# aggregators =
plugins = Aligner RestrictionAnnotator ProteinDumper
# 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
# the reference class is ignored in GFF3 files
# 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.gff3.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
default varying = 1
########################
# 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:example
glyph = generic
strand_arrow = 1
label_position = left
bgcolor = blue
height = 10
category = Genes
key = Example features
[Motifs]
feature = polypeptide_domain
glyph = span
height = 5
description = 1
category = Proteins
key = Example motifs
[Motifs:overview]
feature = polypeptide_domain
glyph = span
height = 5
description = 0
label = 1
key = Motifs
[Alignments]
feature = match
glyph = segments
category = Alignments
key = Example alignments
[Alignments:40000]
glyph = box
[Alignments:50000]
glyph = box
label = 0
bump = 0
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
strand_arrow = 1
description = 1
connector = dashed
category = Alignments
key = Fingerprinted BACs
# There is a new "gene" glyph that draws multipart genes. The "label_transcripts" option
# tells the glyph to draw the name of each individual transcript to the left of its structure.
# The name and description of the gene itself are at the top and bottom of the whole set of
# splice forms.
[Genes]
feature = gene
glyph = gene
bgcolor = peachpuff
description = 1
label_transcripts = 1
#draw_translation = 1
draw_dna = 1
category = Genes
key = Protein-coding genes
# We no longer aggregate CDS objects. Instead we use the mRNA object
# directly. Note that in the GFF3 file, we have to make the mRNAs indexed
# with the Index=1 attribute so that we can access them. Otherwise we can
# only get to them through the gene.
# the ignore_empty_phase option tells the glyph only to draw the phase line
# for subfeatures (i.e. CDS) that have a defined phase. UTRs will be skipped.
[CDS]
feature = mRNA
glyph = cds
height = 30
sixframe = 1
ignore_empty_phase = 1
category = Genes
key = Frame usage
# This is a little tricky. The microarray_oligo data is stored as individual features.
# This prevents the data from being stored as one huge chromosome-wide feature. But we
# have to put the individual data points back together again for the xyplot to work
# properly. So we use the new "group_on" option to tell gbrowse to group the features
# on the display_name() method. (same as name() )
[TransChip]
feature = microarray_oligo
glyph = xyplot
graph_type = boxes
height = 50
min_score = 0
max_score = 1000
scale = right
category = Genes
group_on = display_name
key = Transcriptional Profile
[TransChip:region]
feature = microarray_oligo
glyph = xyplot
graph_type = histogram
height = 50
min_score = 0
max_score = 1000
bgcolor = blue
scale = right
group_on = display_name
key = Profile
# This is almost the same as the gff2 example, except that we take advantage of the new
# label_position option (from Bio::Graphics) to put the label to the left of the glyph
# when the region is <200 bp and on the top of the glyph when the region is >=200 bp
[EST]
feature = EST_match
glyph = segments
height = 10
label_position = left
draw_target = 1
show_mismatch = 1
category = Genes
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
[EST:200]
label = 1
label_position = top
[DNA]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
strand = both
category = Genes
link = ''
gc_window = auto
key = DNA/GC Content
[Traces]
feature = read
glyph = trace
fgcolor = black
bgcolor = orange
strand_arrow = 1
height = 6
description = 1
category = Alignments
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
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
start_codons = 0
stop_codons = 1
category = Proteins
translation = 6frame
key = 6-frame translation
[Translation:30000]
hide = 1
[motif:details]
translation = sub {
my $value = shift;
$value =~ s/(\S{1,60})/$1\n/g;
"$value
";
}
Note = $value
[ProteinDumper:plugin]
geneticcode=12