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the National Human Genome Research Institute and the National Institute of General Medical Sciences.
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[GENERAL]
description = Tribolium castaneum
head =
header =
Tribolium castaneum
# lucegene GFF adaptor
db_adaptor = Bio::DB::GFF
db_args = -adaptor lucene
-dsn ../databases/tribcas/chrs;feats
default_name = scaffold_1:1..50000
default_range = 1-500000
# examples to show in the introduction
examples = LG5:1..50000 LG1=X LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 MT
## need this for Chado segment lookup in Browser.pm _feature_get ...
## reference class = chromosome
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
########## COMMON DROSPEGE GBROWSE.CONF #################
aggregators = processed_transcript genemodel processed_transcript2 alignment
default features = gene
uploads = 1
no uploads = 0
# Web site configuration info; urk FIXME ... installer
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
# region segment = 100000
# advanced features
balloon tips = 0
drag and drop = 1
cache time = 1 # one hour
plugins = BatchDumper FastaDumper GFFDumper ProteinDumper
# FeatureFastaDumper
# max and default segment sizes for detailed view
max segment = 1000001
default segment = 100000
# low-res boundary
low res = 200000
zoom levels = 100 200 1000 2500 5000 10000 25000 50000 75000
100000 150000 200000 300000 500000 1000000
# # where to link to when user clicks in detailed view
link = AUTO
title = sub { my $f= shift;
my $loc= $f->seq_id .':'.$f->start."..".$f->end;
my $ftype= ($f->can("method")) ? $f->method : $f->type;
if ($ftype =~ /^match/) { $ftype= $f->source(); }
my $nm;
if($f->can("attributes")) {
($nm)= grep( /^\w/, $f->attributes('Name'), $f->attributes('Alias'),
$f->attributes('symbol'), $f->attributes('name'), $f->attributes('ID'), $f->name);
} else { $nm= $f->display_name(); }
if($f->can("score")) { my $sc= $f->score; $nm .= " p=$sc" if ($sc =~ /\d/); }
return "$ftype:$nm $loc";
}
#panel property
pad_left = 20
pad_right = 30
key_style = between
grid = 1
# put reversed features on same track or below ?
mix_strand = 1
# colors of the overview, detailed map and key
overview units = M
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
# "automatic" classes to try when an unqualified identifier is given
automatic classes = match
language = en
image widths = 450 640 800 950 1024
default width = 800
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[BatchDumper:plugin]
fileformat = embl
[GFFDumper:plugin]
version = 3
[ProteinDumper:plugin]
fileformat = embl
[TRACK DEFAULTS]
glyph = generic
height = 6
label density = 20
bump density = 50
overview label density = 160
#balloon hover = $name $type at $ref:$start..$end
[gene]
#feature = processed_transcript
# :Tcas_2.0 << dang . remove from gff !!
#glyph = processed_transcript
#feature = mRNA CDS
feature = genemodel
glyph = gene3
bgcolor = lightblue
thin_utr = 1
key = Tribolium genes
category = Genome features
label = sub { my $f = shift;
my($na)= ( $f->attributes('Name'), $f->display_name());
#$na = "NCBI_Gno_".$na if($na =~ m/^\d/); # Parent=gene1234 for each mRNA ID=1234
return $na;
}
[genespan]
#feature = processed_transcript
# :Tcas_2.0 << dang . remove from gff !!
#glyph = processed_transcript
feature = gene
glyph = segments
bgcolor = lightblue
key = Genespan
category = Genome features
[contig]
feature = contig
# :Tcas_2.0
glyph = segments
height = 5
stranded = 1
key = Contig
category = Genome features
balloon hover =
[dna]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
nodump = 1
category = Genome features
key = DNA/GC Content
balloon hover =
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