# gbrowse config file for genome maps
[GENERAL]
description = Drosophila melanogaster dmel_hetr32b_20041025 20041002
datapath = /bio/argos/flybase/genomes/Drosophila_melanogaster/dmel_hetr32b_20041025/gnomap
browser title = Genome Browser
help = /maps/gbrowse
# adaptor = flybase::gmod::FFFdb
adaptor =
default_name = 2h:1..100000
# X:100000-200000
default_range = 1-500000
# examples to show in the introduction
examples = 2h: 3h: 4h: U: Xh: Yh:
header = Genome Browser
footer =
Adapted from GBrowse of the
Generic Model Organism Database Project.
debug = 0
plugins = BatchDumper FastaDumper
#fixme ...
default features = rev_ruler cytoband gene tRNA noncodingRNA golden_path segment BAC transposable_element pseudogene
primary_feature = gene
scale_feature = cytoband
dumpviews = FastA GenBank GFF
dataviews = "Default" "Collapse All" "Expand All"
# Web site configuration info
stylesheet = /templates/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 = bottom
key bgcolor = whitesmoke
grid = 1
overview bgcolor = whitesmoke
# # where to link to when user clicks in detaild view
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
# put reversed features on same track or below ?
mix_strand = 1
# 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"
link =
[chromosome_arm]
feature = chromosome_arm
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = chromosome_arm
citation = chromosome_arm
keygroup = "Analysis features"
link =
[five_prime_UTR]
feature = five_prime_UTR
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = five_prime_UTR
citation = five_prime_UTR
keygroup = "Analysis features"
link =
[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 '' ; }
[intron]
feature = intron
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = intron
citation = intron
keygroup = "Analysis features"
link =
[mRNA]
feature = mRNA
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = mRNA
citation = mRNA
keygroup = "Analysis features"
link =
[match:HDP]
feature = match:HDP
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:HDP
citation = match:HDP
keygroup = "Analysis features"
link =
[match:blastx:aa_SP.hyp.dros]
feature = match:blastx:aa_SP.hyp.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SP.hyp.dros
citation = match:blastx:aa_SP.hyp.dros
keygroup = "Analysis features"
link =
[match:blastx:aa_SP.real.dros]
feature = match:blastx:aa_SP.real.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SP.real.dros
citation = match:blastx:aa_SP.real.dros
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.dros]
feature = match:blastx:aa_SPTR.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.dros
citation = match:blastx:aa_SPTR.dros
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.insect]
feature = match:blastx:aa_SPTR.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.insect
citation = match:blastx:aa_SPTR.insect
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.othinv]
feature = match:blastx:aa_SPTR.othinv
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.othinv
citation = match:blastx:aa_SPTR.othinv
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.othvert]
feature = match:blastx:aa_SPTR.othvert
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.othvert
citation = match:blastx:aa_SPTR.othvert
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.plant]
feature = match:blastx:aa_SPTR.plant
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.plant
citation = match:blastx:aa_SPTR.plant
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.primate]
feature = match:blastx:aa_SPTR.primate
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.primate
citation = match:blastx:aa_SPTR.primate
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.rodent]
feature = match:blastx:aa_SPTR.rodent
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.rodent
citation = match:blastx:aa_SPTR.rodent
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.worm]
feature = match:blastx:aa_SPTR.worm
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.worm
citation = match:blastx:aa_SPTR.worm
keygroup = "Analysis features"
link =
[match:blastx:aa_SPTR.yeast]
feature = match:blastx:aa_SPTR.yeast
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_SPTR.yeast
citation = match:blastx:aa_SPTR.yeast
keygroup = "Analysis features"
link =
[match:blastx:aa_TR.real.dros]
feature = match:blastx:aa_TR.real.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_TR.real.dros
citation = match:blastx:aa_TR.real.dros
keygroup = "Analysis features"
link =
[match:blastx:aa_users_i.dros]
feature = match:blastx:aa_users_i.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:blastx:aa_users_i.dros
citation = match:blastx:aa_users_i.dros
keygroup = "Analysis features"
link =
[match:genscan]
feature = match:genscan
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:genscan
citation = match:genscan
keygroup = "Analysis features"
link =
[match:groupest:na_DGC.dros]
feature = match:groupest:na_DGC.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:groupest:na_DGC.dros
citation = match:groupest:na_DGC.dros
keygroup = "Analysis features"
link =
[match:groupest:na_EST.all_nr.dros]
feature = match:groupest:na_EST.all_nr.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:groupest:na_EST.all_nr.dros
citation = match:groupest:na_EST.all_nr.dros
keygroup = "Analysis features"
link =
[match:groupest:na_EST.complete.dros]
feature = match:groupest:na_EST.complete.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:groupest:na_EST.complete.dros
citation = match:groupest:na_EST.complete.dros
keygroup = "Analysis features"
link =
[match:piecegenie]
feature = match:piecegenie
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:piecegenie
citation = match:piecegenie
keygroup = "Analysis features"
link =
[match:piler]
feature = match:piler
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:piler
citation = match:piler
keygroup = "Analysis features"
link =
[match:piler_raw]
feature = match:piler_raw
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:piler_raw
citation = match:piler_raw
keygroup = "Analysis features"
link =
[match:promoter]
feature = match:promoter
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:promoter
citation = match:promoter
keygroup = "Analysis features"
link =
[match:repeat_runner_seg]
feature = match:repeat_runner_seg
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:repeat_runner_seg
citation = match:repeat_runner_seg
keygroup = "Analysis features"
link =
[match:sim4:P_U.fa]
feature = match:sim4:P_U.fa
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:P_U.fa
citation = match:sim4:P_U.fa
keygroup = "Analysis features"
link =
[match:sim4:gad_mrna.r3]
feature = match:sim4:gad_mrna.r3
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:gad_mrna.r3
citation = match:sim4:gad_mrna.r3
keygroup = "Analysis features"
link =
[match:sim4:na_ARGsregion.dros]
feature = match:sim4:na_ARGsregion.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_ARGsregion.dros
citation = match:sim4:na_ARGsregion.dros
keygroup = "Analysis features"
link =
[match:sim4:na_DGC.dros]
feature = match:sim4:na_DGC.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_DGC.dros
citation = match:sim4:na_DGC.dros
keygroup = "Analysis features"
link =
[match:sim4:na_DGC.in_process.dros]
feature = match:sim4:na_DGC.in_process.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_DGC.in_process.dros
citation = match:sim4:na_DGC.in_process.dros
keygroup = "Analysis features"
link =
[match:sim4:na_EST.all_nr.dros]
feature = match:sim4:na_EST.all_nr.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_EST.all_nr.dros
citation = match:sim4:na_EST.all_nr.dros
keygroup = "Analysis features"
link =
[match:sim4:na_EST.complete.dros]
feature = match:sim4:na_EST.complete.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_EST.complete.dros
citation = match:sim4:na_EST.complete.dros
keygroup = "Analysis features"
link =
[match:sim4:na_STS.dros]
feature = match:sim4:na_STS.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_STS.dros
citation = match:sim4:na_STS.dros
keygroup = "Analysis features"
link =
[match:sim4:na_cDNA.dros]
feature = match:sim4:na_cDNA.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_cDNA.dros
citation = match:sim4:na_cDNA.dros
keygroup = "Analysis features"
link =
[match:sim4:na_gadfly.dros.RELEASE2]
feature = match:sim4:na_gadfly.dros.RELEASE2
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_gadfly.dros.RELEASE2
citation = match:sim4:na_gadfly.dros.RELEASE2
keygroup = "Analysis features"
link =
[match:sim4:na_gb.dmel]
feature = match:sim4:na_gb.dmel
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_gb.dmel
citation = match:sim4:na_gb.dmel
keygroup = "Analysis features"
link =
[match:sim4:na_gb.dros]
feature = match:sim4:na_gb.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_gb.dros
citation = match:sim4:na_gb.dros
keygroup = "Analysis features"
link =
[match:sim4:na_pe.dros]
feature = match:sim4:na_pe.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_pe.dros
citation = match:sim4:na_pe.dros
keygroup = "Analysis features"
link =
[match:sim4:na_snRNA.dros]
feature = match:sim4:na_snRNA.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:na_snRNA.dros
citation = match:sim4:na_snRNA.dros
keygroup = "Analysis features"
link =
[match:sim4:r3_noncoding.FASTA]
feature = match:sim4:r3_noncoding.FASTA
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:sim4:r3_noncoding.FASTA
citation = match:sim4:r3_noncoding.FASTA
keygroup = "Analysis features"
link =
[match:tblastx:P_U.fa]
feature = match:tblastx:P_U.fa
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:tblastx:P_U.fa
citation = match:tblastx:P_U.fa
keygroup = "Analysis features"
link =
[match:tblastx:na_dbEST.insect]
feature = match:tblastx:na_dbEST.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:tblastx:na_dbEST.insect
citation = match:tblastx:na_dbEST.insect
keygroup = "Analysis features"
link =
[match:tblastx:na_unigene.rodent]
feature = match:tblastx:na_unigene.rodent
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = match:tblastx:na_unigene.rodent
citation = match:tblastx:na_unigene.rodent
keygroup = "Analysis features"
link =
[ncRNA]
feature = ncRNA
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = ncRNA
citation = ncRNA
keygroup = "Analysis features"
link =
[pseudogene]
feature = pseudogene
glyph = segments
strand_arrow = 1
fgcolor = orange
label = 1
key = Pseudogene
keygroup = " Genomic features"
[rRNA]
feature = rRNA
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = rRNA
citation = rRNA
keygroup = "Analysis features"
link =
[repeat_region]
feature = repeat_region
bgcolor = darkorchid
fgcolor = darkorchid
height = 3
connector = solid
bump = 1
strand_arrow = 0
label = 0
key = Repeat region
citation = repeat_region (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[source]
feature = source
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = source
citation = source
keygroup = "Analysis features"
link =
[three_prime_UTR]
feature = three_prime_UTR
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = three_prime_UTR
citation = three_prime_UTR
keygroup = "Analysis features"
link =
[transposable_element]
feature = transposable_element
bgcolor = magenta
fgcolor = magenta
label = 1
glyph = anchored_arrow
key = Natural transposon
citation = Natural transposon (annotation DB ; Chado)
keygroup = " Genomic features"
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 =~ /^TE/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
}
if ($f->name()) { return '/cgi-bin/fbinsq.html?symbol='.$f->name(); }
return '' ; }