# gbrowse config file for  genome maps

[GENERAL]
description = Drosophila melanogaster dmel_r3.2.2_10212004 20041002
datapath    = /bio/argos/flybase/genomes/Drosophila_melanogaster/dmel_r3.2.2_10212004/gnomap

browser title = Genome Browser
help = /maps/gbrowse

# adaptor     = flybase::gmod::FFFdb
adaptor     =  

default_name = 2L:1..100000 
# X:100000-200000
default_range = 1-500000

# examples to show in the introduction
examples =  2L: 2R: 3L: 3R: 4: U: X: 

header = Genome Browser
footer = <hr>
 Adapted from GBrowse of the <a href="http://www.gmod.org/">
 Generic Model Organism Database Project.</a>

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] ------------------------
  
[BAC]
feature  = BAC
glyph         = extending_arrow
no_arrows     = 1
base          = 0
bgcolor       = lightslategray
fgcolor       = lightslategray
linewidth     = 2
bump          = 1
label         = 1
key           = Tiling BAC
citation     = BAC (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
 return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; }


[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 =


[DNA_motif]
feature  = DNA_motif RNA_motif
bgcolor       = plum
fgcolor       = plum
secondary     = RNA_motif
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
strand_arrow  = 1
bump          = 1
label         = 0
key           = DNA / RNA motif
citation     = DNA_motif and RNA_motif (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"


[RNA_motif]
feature  = RNA_motif
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = RNA_motif
citation = RNA_motif
keygroup = "Analysis features"
link     =


[aberration_junction]
feature  = aberration_junction
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = aberration_junction 
citation     = aberration_junction (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[chromosome_arm]
feature  = chromosome_arm
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = chromosome_arm
citation = chromosome_arm
keygroup = "Analysis features"
link     =


[chromosome_band]
feature  = chromosome_band
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = chromosome_band
citation = chromosome_band
keygroup = "Analysis features"
link     =


[cytobreakpoint_inv]
feature       = cytobreakpoint_inv
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #FF9900
bump          = 1
label         = 1
key						= Inversion breakpoints (cytol.)
citation     	= Inversion breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"


[cytobreakpoint_other]
feature       = cytobreakpoint_other
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #8888FF
bump          = 1
label         = 1
key						= Other breakpoints (cytol.)
citation     	= Other breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"


[cytobreakpoint_ttp]
feature       = cytobreakpoint_ttp
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
bump          = 1
label         = 1
key						= Translocations & Transpositions (cytol.)
citation     	= Translocation & Transposition breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"


[cytodeleted_segment]
feature       = cytodeleted_segment
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #ff00aa
bump          = 1
label         = 1
key						= Deleted segments (cytol.)
citation     	= Deleted segments (cytology mapped)
height        = 2
keygroup 			= "Cytology mapped features"


[cytoduplicated_segment]
feature       = cytoduplicated_segment
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #88FF88
bump          = 1
label         = 1
key						= Duplicated segments (cytol.)
citation     	= Duplicated segments (cytology mapped)
height        = 2
keygroup 			= "Cytology mapped features"


[cytogene]
feature       = cytogene
glyph         = cytobar
connector = dashed
connector_color = #ffaa00
bgcolor       = lightslategray
fgcolor       = lightslategray
connector = dashed
bump          = 1
label         = 1
key           = Gene (recomb. only)
citation      = Genes mapped by cytology/recombination data only (possible orphans; cytologically mapped; CytoSearch DB)
height        = 4
keygroup = "Cytology mapped features"


[cytoins]
feature       = cytoins
glyph         = cytobar
connector_color = #ffbb00
bgcolor       = lightslategray
fgcolor       = lightslategray
connector = dashed
bump          = 1
label         = 1
key	= Transgene insertion (cytol.)
citation     = Chromosomal Insertion (cytologically mapped; CytoSearch DB)
height        = 2
keygroup 			= "Cytology mapped features"


[enhancer]
feature  = enhancer
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = enhancer 
citation     = enhancer (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[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 '' ; }


[insertion_site]
feature  = insertion_site
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = insertion_site
citation = insertion_site
keygroup = "Analysis features"
link     =


[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     =


[mRNA:genscan]
feature  = mRNA:genscan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA:genscan
citation = mRNA:genscan
keygroup = "Analysis features"
link     =


[mRNA:piecegenie]
feature  = mRNA:piecegenie
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA:piecegenie
citation = mRNA:piecegenie
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:RNAiHDP]
feature  = match:RNAiHDP
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:RNAiHDP
citation = match:RNAiHDP
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SP.hyp.dros]
feature  = match:blastx_masked:aa_SP.hyp.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SP.hyp.dros
citation = match:blastx_masked:aa_SP.hyp.dros
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SP.real.dros]
feature  = match:blastx_masked:aa_SP.real.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SP.real.dros
citation = match:blastx_masked:aa_SP.real.dros
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.dros]
feature  = match:blastx_masked:aa_SPTR.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.dros
citation = match:blastx_masked:aa_SPTR.dros
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.insect]
feature  = match:blastx_masked:aa_SPTR.insect
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.insect
citation = match:blastx_masked:aa_SPTR.insect
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.othinv]
feature  = match:blastx_masked:aa_SPTR.othinv
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.othinv
citation = match:blastx_masked:aa_SPTR.othinv
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.othvert]
feature  = match:blastx_masked:aa_SPTR.othvert
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.othvert
citation = match:blastx_masked:aa_SPTR.othvert
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.plant]
feature  = match:blastx_masked:aa_SPTR.plant
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.plant
citation = match:blastx_masked:aa_SPTR.plant
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.primate]
feature  = match:blastx_masked:aa_SPTR.primate
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.primate
citation = match:blastx_masked:aa_SPTR.primate
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.rodent]
feature  = match:blastx_masked:aa_SPTR.rodent
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.rodent
citation = match:blastx_masked:aa_SPTR.rodent
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.worm]
feature  = match:blastx_masked:aa_SPTR.worm
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.worm
citation = match:blastx_masked:aa_SPTR.worm
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_SPTR.yeast]
feature  = match:blastx_masked:aa_SPTR.yeast
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_SPTR.yeast
citation = match:blastx_masked:aa_SPTR.yeast
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_TR.real.dros]
feature  = match:blastx_masked:aa_TR.real.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_TR.real.dros
citation = match:blastx_masked:aa_TR.real.dros
keygroup = "Analysis features"
link     =


[match:blastx_masked:aa_users_i.dros]
feature  = match:blastx_masked:aa_users_i.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx_masked:aa_users_i.dros
citation = match:blastx_masked:aa_users_i.dros
keygroup = "Analysis features"
link     =


[match:fgenesh]
feature  = match:fgenesh
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:fgenesh
citation = match:fgenesh
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_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_adh.cDNAs.dros]
feature  = match:sim4:na_adh.cDNAs.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_adh.cDNAs.dros
citation = match:sim4:na_adh.cDNAs.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.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: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     =


[mature_peptide]
feature  = mature_peptide
glyph = segments
strand_arrow  = 1
bgcolor = palegoldenrod
fgcolor       = orange
label = 1
key  = mature_peptide
citation     = mature_peptide (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
  }


[ncRNA]
feature  = ncRNA
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = ncRNA
citation = ncRNA
keygroup = "Analysis features"
link     =


[oligo]
feature  = oligo
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = oligo
citation = oligo
keygroup = "Analysis features"
link     =


[orthologous_region]
feature  = orthologous_region
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = orthologous_region
citation = orthologous_region
keygroup = "Analysis features"
link     =


[point_mutation]
feature  = point_mutation
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = point_mutation 
citation     = point_mutation (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
 
 
[protein_binding_site]
feature  = protein_binding_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = protein_binding_site 
citation     = protein_binding_site (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[polyA_site]
feature  = polyA_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = polyA_site 
citation     = polyA_site (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[protein_binding_site]
feature  = protein_binding_site
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = protein_binding_site
citation = protein_binding_site
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     =


[region]
feature  = region
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = region
citation = region
keygroup = "Analysis features"
link     =


[regulatory_region]
feature  = regulatory_region
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = regulatory_region 
citation     = regulatory_region (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[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 =


[rescue_fragment]
feature  = rescue_fragment
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = rescue_fragment 
citation     = rescue_fragment (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[scaffold]
## aug04 - renamed to SO equivalent golden_path; 
## sep04 - golden_path_fragment is better, or supercontig ?
feature  = scaffold golden_path_fragment 
glyph         = anchored_arrow
no_arrows     = 1
base          = 0
fgcolor       = black
bgcolor       = black
linewidth     = 2
bump          = 1
label         = 1
height        = 4
key           = GenBank Scaffold
citation     = genbank submission unit, a golden_path_fragment  (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
 return ($f->name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; }


[sequence_variant]
feature  = sequence_variant
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = sequence_variant 
citation     = sequence_variant (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }


[snRNA]
feature  = snRNA
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = snRNA
citation = snRNA
keygroup = "Analysis features"
link     =


[snoRNA]
feature  = snoRNA
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = snoRNA
citation = snoRNA
keygroup = "Analysis features"
link     =


[source]
feature  = source
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = source
citation = source
keygroup = "Analysis features"
link     =


[syntenic_region]
feature  = syntenic_region
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = syntenic_region
citation = syntenic_region
keygroup = "Analysis features"
link     =


[tRNA]
feature  = tRNA
glyph = transcript2
label = 1
stranded     = 1
bgcolor      = white
fgcolor      = black
curatedexon  = slateblue
fontcolor    = slateblue
key          = tRNA
keygroup = "  Genomic features"
citation     = These are tRNA predictions made using Sean Eddy's tRNAscan program.


[tRNA:trnascan]
feature  = tRNA:trnascan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = tRNA:trnascan
citation = tRNA:trnascan
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     =


[transcription_start_site]
feature  = transcription_start_site
glyph         = promoter
bgcolor       = purple
fgcolor       = purple
bump          = 1
label         = 0
key = Promoter prediction
citation     = Transcription promoter prediction (annotation DB ; Chado)
keygroup = "Analysis features"


[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 '' ; }


[transposable_element_insertion_site]
feature  = transposable_element_insertion_site
glyph         = pinsertion
bgcolor       = darkturquoise
fgcolor       = darkturquoise
bump          = 1
label         = 0
key           = Transgene insertion site
citation     = Transgene insertion site (annotation DB ; Chado)
keygroup = "  Genomic features"


[transposable_element_pred]
feature  = transposable_element_pred
bgcolor       = tan
fgcolor       = brown
label = 1
glyph         = anchored_arrow
key           = Transposon prediction
citation     = Transposon prediction (annotation DB ; Chado)
keygroup = "Analysis features"
link =