# gbrowse config file for genome maps
[GENERAL]
description = Drosophila pseudoobscura r1.04
datapath = /bio/argos/flybase/genomes/Drosophila_pseudoobscura/dpse_r10_20041216/gnomap
browser title = Genome Browser
adaptor = flybase::gmod::FFFdb
default_name = 2:1..100000
# X:100000-200000
default_range = 1-500000
# examples to show in the introduction
# examples = 2: 2L: 2R: 2_groupMISC: 3: 3L: 3R: 3_groupMISC: 4: 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: 4_groupMISC: 5_groupMISC: U: X: XL_group1a: XL_group1e: XL_group3a: XL_group3b: XL_groupMISC: XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: XR_groupMISC:
chromosomes = 2: 2L: 2R: 2_groupMISC: 3: 3L: 3R: 3_groupMISC: 4: 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: 4_groupMISC: 5_groupMISC: U: X: XL_group1a: XL_group1e: XL_group3a: XL_group3b: XL_groupMISC: XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: XR_groupMISC:
header =
FlyBase Genome Browser: Drosophila pseudoobscura
Release r1.04; 20041216
footer =
Adapted from GBrowse of the
Generic Model Organism Database Project.
plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper
# GFFDumper - not as good as BatchDumper
# OligoFinder - requires Bio::DB::GFF sql calls
uploads = 1
#fixme ...
default features = rev_ruler cytoband gene tRNA noncodingRNA pseudogene
syntenic_region scaffold BAC transposable_element
primary_feature = gene
scale_feature = cytoband
dumpviews = FastA GenBank GFF FFF
dataviews = "Default" "Collapse All" "Expand All"
# Web site configuration info
help = /common/perl/gbrowse_fb/htdocs
stylesheet = /common/perl/gbrowse_fb/gbrowse.css
buttons = /common/perl/gbrowse_fb/images/buttons
tmpimages = /tmp/gbrowse_fb
# max and default segment sizes for detailed view
max segment = 1000001
default segment = 100000
## base range to expand around gene given ID lookup
expand_by = 20000
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
searchhelp = Search using Chromosome:base_start..end or FlyBase Gene ID.
#panel property
pad_left = 20
pad_right = 30
key_style = between
key bgcolor = whitesmoke
overview bgcolor = whitesmoke
grid = 1
# put reversed features on same track or below ?
mix_strand = 1
# # where to link to when user clicks in detaild view
# # default dummy link to get popup title view
link = sub { return "#"; }
# link = sub {
# my $f= shift;
# my $d= $f->primary_id() if $f->can('primary_id');
# $d= $f->source() unless($d);
# if ($d) {
# if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
# elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
# elsif ($d =~ /\-\w+/ ){ return '/cgi-bin/fbannq.html?'.$d; }
# }
# if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); }
# return '' ; }
title = sub { my $f= shift;
return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
}
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
# Default glyph settings
glyph = generic
height = 5
bgcolor = palegoldenrod
fgcolor = cyan
boxcolor = blue
label density = 20
bump density = 50
overview label density = 160
image widths = 450 640 800 950 1024
default width = 800
width = 800
#---------- end [GENERAL] ------------------------
[CDS]
feature = CDS
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = 1
key = CDS
citation = Protein coding sequence (CDS or translation; annotation DB ; Chado)
keygroup = " Genomic features"
[chromosome_arm]
feature = chromosome_arm
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = chromosome_arm
citation = chromosome_arm
keygroup = "Analysis features"
[gene]
feature = gene mRNA
glyph = transcript2
bgcolor = lightblue
fgcolor = blue
secondary = mRNA
secondary_bgcolor = mediumblue
secondary_fgcolor = mediumblue
highlight_color = red
higlighted = 1
label = 1
label density = 50
key = Gene Model
keygroup = " Genomic features"
citation = Gene and mRNA (transcript) features (annotation DB ; Chado)
link = sub {
my $f= shift;
my $d= $f->primary_id() if $f->can('primary_id');
$d= $f->source() unless($d);
if ($d) {
if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
}
if ($f->name()) { return '/cgi-bin/fbgenq.html?symbol='.$f->name(); }
return '' ; }
[gene:genewise]
feature = gene:genewise
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = gene:genewise
citation = gene:genewise
keygroup = "Analysis features"
[gene:genscan]
feature = gene:genscan
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = gene:genscan
citation = gene:genscan
keygroup = "Analysis features"
[gene:twinscan]
feature = gene:twinscan
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = gene:twinscan
citation = gene:twinscan
keygroup = "Analysis features"
[golden_path]
feature = golden_path
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = golden_path
citation = golden_path
keygroup = "Analysis features"
[golden_path_fragment]
feature = golden_path_fragment
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = golden_path_fragment
citation = golden_path_fragment
keygroup = "Analysis features"
[intron]
feature = intron
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = intron
citation = intron
keygroup = "Analysis features"
[mRNA]
feature = mRNA
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = mRNA
citation = mRNA
keygroup = "Analysis features"
[mRNA:genewise]
feature = mRNA:genewise
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = mRNA:genewise
citation = mRNA:genewise
keygroup = "Analysis features"
[mRNA:genscan]
feature = mRNA:genscan
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = mRNA:genscan
citation = mRNA:genscan
keygroup = "Analysis features"
[mRNA:twinscan]
feature = mRNA:twinscan
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = mRNA:twinscan
citation = mRNA:twinscan
keygroup = "Analysis features"
[match:blastn:na_dbEST.dpse]
feature = match:blastn:na_dbEST.dpse
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastn:na_dbEST.dpse
citation = match:blastn:na_dbEST.dpse
keygroup = "Analysis features"
[match:blastz]
feature = match:blastz
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastz
citation = match:blastz
keygroup = "Analysis features"
[orthologous_region]
feature = orthologous_region
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = orthologous_region
citation = orthologous_region
keygroup = "Analysis features"
[source]
feature = source
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = source
citation = source
keygroup = "Analysis features"
[supercontig]
feature = supercontig
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = supercontig
citation = supercontig
keygroup = "Analysis features"
[syntenic_region]
feature = syntenic_region
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = syntenic_region
citation = syntenic_region
keygroup = "Analysis features"