# flybase.conf
# 
# strelets@flybase.org

[GENERAL]
description = D. melanogaster Genome (R5.2)
organism    = D. melanogaster
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
	              -dsn dbi:mysql:database=flybase

###########################################################################################

source = dmel

# The class of the feature that is used as the reference for all others
# "Sequence" is the default - change it if you use something else
default class = Sequence

initial landmark = cnn

# "automatic" classes to try when an unqualified identifier is given
automatic classes = gene mRNA CDS noncodingRNA tRNA transposable_element transposable_element_insertion_site cDNA_1

# default width of detailed view (pixels)
default width = 800
default features =  gene mRNA CDS noncodingRNA tRNA transposable_element transposable_element_insertion_site cDNA_1

too many features = 5000

# examples to show in the introduction
examples = 
		cnn
		FBgn0000490 
    X:60000..80000
    2L:80,000..100,000
    2R:80,000..100,000
    3L:80,000..100,000
    3R:80,000..100,000
    4:20000..50000

# Installed plugins
plugins = FBTableDumper
					FastaDumper
          GFFDumper
					FBGenbankDumper

cache_overview = 360
cachedir = 360

# Web site configuration info
stylesheet  = /common/perl/gbrowse/gbrowse.css
buttons     = /common/perl/gbrowse/images/buttons
tmpimages   = /tmp/gbrowse
help     = /gbrowse/
#link_target   = _new

default varying = 1 # track appear as defined below, not in alphabetical order

# Default glyph settings
glyph       = generic
height      = 8
label density = 25
bump density  = 100

# where to link to when user clicks in detaild view
# generic FB link - should work if FB id is in data
link = sub {
  (my $f)= shift;
	#warn "\n"; foreach( keys %$f ) { warn "   ft ".$_." = ".$f->{$_}."\n"; }
  (my $tp)= $f->{'type'};
  (my $best)='(FB\w\w\d+)';
  if($tp =~ /^gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
  elsif($tp =~ /^(mRNA|CDS|exon|intron)/i) { $best='(FBtr\d+)'; }
  elsif($tp =~ /UTR/i) { $best='(FBtr\d+)'; }
  elsif($tp =~ /^(transposable_element)/i) { $best='(FBti\d+)'; }
  elsif($tp =~ /^cyto/i) { $best='(FB(gn|ab|ba)\d+)'; }
  (my $id)= $f->{'id'};
  if ($id =~ /$best/){ return '/cgi-bin/fbidq.html?'.$1; }
  elsif ($id =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
  elsif ($id =~ /((C[GR]|TE|GA)\d+)/ ){ return '/cgi-bin/fbidq.html?'.$1; }
	# last resort
  if ($id) { return '/cgi-bin/fbidq.html?'.$id; } 
  }

title = sub { my $f= shift;
    (my $name) = $f->{'ftname'};
		return($name);
		}
		
# which image widths to offer
image widths  = 640 800 1024

# max and default segment sizes for detailed view
max segment = 1000001
default segment = 20000

# low-res boundary
low res = 200000

# zoom levels
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 100000 200000

# colors of the overview, detailed map and key
overview units   = M

language = en


# Various places where you can insert your own HTML -- see configuration docs
#no search = yes
html1 = 
html2 =
html3 = 
html4 = 
html5 = 
html6 = 	
  
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks


#---------- Sequence -----------------

[TranslationF]
glyph        = translation
global feature = 1
frame0       = cadetblue
frame1       = blue
frame2       = darkblue
height       = 20
fgcolor      = purple
strand       = +1
translation  = 3frame
key          = 3-frame translation (forward)

[DNA/GC Content]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
fgcolor      = red
axis_color   = blue

[TranslationR]
glyph        = translation
global feature = 1
frame0       = darkred
frame1       = red
frame2       = crimson
height       = 20
fgcolor      = blue
strand       = -1
translation  = 3frame
key          = 3-frame translation (reverse)

#------------- GENOMIC FEATURES --------------------

[gene]
feature       = gene 
glyph 				= generic
stranded 			= 1
bgcolor       = lightblue
fgcolor       = blue
highlight_color = red
higlighted = 1
label density = 50
bump density  = 150
key           = Gene Span
category = "Gene Model features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
title= ""
link = sub { my $f= shift;
  my $id= $f->{'id'};
	"/cgi-bin/fbidq.html?$id";
	}

[mRNA]
feature  = mRNA
glyph = processed_transcript
bgcolor = peachpuff
connector = solid
stranded = 1
translation  = 1frame
key  = mRNA
category = "Gene Model features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[five_prime_UTR]
feature  = five_prime_UTR
glyph = segments
bgcolor = peachpuff
connector = solid
stranded = 1
translation  = 1frame
key  = five_prime_UTR
category = "Gene Model features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[three_prime_UTR]
feature  = three_prime_UTR
glyph = segments
bgcolor = peachpuff
connector = solid
stranded = 1
translation  = 1frame
key  = three_prime_UTR
category = "Gene Model features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[exon]
feature  = exon
glyph = segments
bgcolor = peachpuff
connector = solid
stranded = 1
translation  = 1frame
key  = exon
category = "Gene Model features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[protein]
feature  = CDS
glyph = segments
connector = solid
stranded     = 1
translation  = 1frame
bgcolor = lightgrey
fgcolor = goldenrod
key  = protein
category = "Gene Model features"
link = sub { my $f = shift; (my $id) = $f->name(); return('/cgi-bin/fbidq.html?'.$id); }
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[CDS]
feature  = CDS
glyph = segments
connector = solid
stranded     = 1
translation  = 1frame
bgcolor = lightgrey
fgcolor = goldenrod
key  = CDS
category = "Gene Model features"
link = sub { my $f = shift; (my $id) = $f->name(); return('/cgi-bin/fbidq.html?'.$id); }
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

#-------- Synteny -------------------

[orthologFB]
feature  = orthologous_to
glyph    = segments
bgcolor = palegoldenrod
fgcolor = turquoise
label density = 50
height        = 4
key  = Ortholog (FlyBase)
category = "Similarity: Synteny features"
link = sub {  (my $f)= shift;
  (my $nt)= $f->{'note'};
  (my $linkurl)= '/cgi-bin/gbrowse/';
  (my $species)= 'dmel';
  #to_name=FBgn0001002;to_species=dpse
  if($nt =~ m/to_species=([^;,]+)/) { $species= $1; }
  my $link= $linkurl.lc($species);
  if( $nt=~/to_id=(FB[a-z]{2}\d+)/ ) {
    $link.= '/?Search=1;id='.$1;
    return($link);
    }
  if( $nt=~/Name=Dpse\\([^;]+)/i ) {
    my $sym=$1; $sym=~s/-[PR][A-Z]$//;
    $link;
    }
  return($link);
  }
label = sub {  (my $f)= shift;
  (my $nt)= $f->{'note'};
  (my $name)= "";
  (my $species)= 'dmel';
  #to_name=FBpp0001002,CG31119-PA;to_species=dmel
  if($nt =~ m/to_species=([^;,]+)/) { $species= $1; }
  if( $nt=~/Name=Dpse\\([^;]+)/i ) { $name= $species.'\\'.$1; }
  elsif ($nt =~ m/to_id=(ortho[^;]+)/i) { $name= $species.'\\'.$1; }
  return($name);
  }

[synteny]
feature  = syntenic_region
glyph = segments
bgcolor = pink
fgcolor = darkred
height        = 4
key  = Syntenic region (FlyBase)
category = "Similarity: Synteny features"
label = sub {  (my $f)= shift; 
  (my $nt)= $f->{'note'};
	(my $species)= 'dmel';
  #to_species=dmel
  if($nt =~ m/to_species=([^;,]+)/) { $species= $1; }
	return($species.'\\'.$f->{'id'});
  }
link = 

[orthologGLEANR]
feature  = putative_ortholog
glyph    = segments
bgcolor = palegoldenrod
fgcolor = turquoise
label density = 50 
height        = 4
key  = Ortholog (GLEANR)
category = "Similarity: Synteny features"
link = sub {  (my $f)= shift; 
  (my $nt)= $f->{'note'};
	(my $linkurl)= "/cgi-bin/gbrowse/";
	(my $species)= 'dmel';
  #to_name=FBpp0001002,CG31119-PA;to_species=dmel
  if($nt =~ m/to_species=([^;,]+)/) { $species= $1;  }
  if ($nt =~ m/ID=([^;]+)/i) { return($linkurl.$species.'/?Search=1;name='.$1); }
	return("");
  }
label = sub {  (my $f)= shift; 
  (my $nt)= $f->{'note'};
	(my $name)= "";
	(my $species)= 'dmel';
  #to_name=FBpp0001002,CG31119-PA;to_species=dmel
  if($nt =~ m/to_species=([^;,]+)/) { $species= $1; }
  if ($nt =~ m/Name=([^;]+)/i) { $name= $1; }
	return($name);
  }

#--------- Genomic features ----------------

[chromosome_band]
feature      = chromosome_band
#glyph        = generic
glyph = anchored_arrow
fgcolor = black
bgcolor = black
height       = 4
key  = Cytological band
category = "Genomic features"
label = sub { my $f = shift; my $name= $f->{'ftname'}; 
	if($name=~/band[\-\_]([0-9A-Z]+)/i) { return($1); } else { return($name); } }
link = sub {
  (my $f)= shift;
	(my $name)= $f->{'ftname'};
	if($name=~/band[\-\_]([0-9A-Z]+)/i) { 
		return '/cgi-bin/txtbrowse_fb.html?xfieldname1=CLOC&xfield1='.$1; }
	else { return ""; } 
  }

[tRNA]
feature      = tRNA
bgcolor      = white
fgcolor      = black
curatedexon  = slateblue
fontcolor    = slateblue
height       = 4
key          = tRNA
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
category = "Genomic features"

[noncodingRNA]
feature      = ncRNA snoRNA snRNA miRNA
glyph        = segments
bgcolor      = peachpuff
height       = 4
stranded     = 1
key          = Non coding RNA
category = "Genomic features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[transposable_element]
feature  = transposable_element
bgcolor       = magenta
fgcolor       = magenta
glyph         = anchored_arrow
key           = Natural transposon
category = "Genomic features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }

[transposable_element_insertion_site]
feature  = transposable_element_insertion_site
glyph         = pinsertion
bgcolor       = darkturquoise
fgcolor       = darkturquoise
bump          = 1
key           = Transgene insertion site
category = "Genomic features"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
title= ""
link = sub { my $f= shift;
  my $id= $f->{'id'};
  my $d= join(',',$id,$f->{'dbxref'});
	my $link;  
  if ($d =~ /(FBti\d+)/ || $d =~ /((FB\w\w|TE)\d+)/) { $link= '/cgi-bin/fbidq.html?'.$1; }
  elsif ($f->{'ftname'}) { $link= '/cgi-bin/fbinsq.html?symbol='.$f->{'ftname'}; }
	my $data= $f->{'gff_string'};
	$data=~s/([^0-9\@A-Z_a-z\/\*\-])/sprintf("%%%02X",ord($1))/eg;
	$link;
	}

#---------- Genome reagents and data --------------

[cDNA_1]
feature  = sim4_na_gb.dmel sim4_na_gb.tpa.dmel sim4tandem_na_gb.dmel splign_na_cDNA_ncbi
glyph         = segments
bgcolor       = sub { my $f = shift; 
	my $v=$f->{'gff_string'};
	my $color= 'darkgreen'; 
	if( 0 && $v=~/target_type=so/ ) { $color= 'lightgreen'; } 
	return $color; 
	}
fgcolor       = darkgreen
strand_arrow  = 1
linewidth     = 2
key     = cDNA and Aligned genomic sequences 
category = "Genome reagents and data"
label = sub { my $f = shift; 
	(my $name) = $f->{'ftname'}; 
	my $v=$f->{'gff_string'}; 
	if( $v=~/Target=([^ \t;]+)[ \t;]/ ) { $name= $1; }  
	return $name; 
	}
link = sub { my $f = shift;
	my $v=$f->{'gff_string'}; 
	if( $v=~/Target=([^ \t;]+)[ \t;]/ ) {   
  	return 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&tool=FlyBase&val='.$1; }
	return("");  
  }

[EST_1]
feature       = sim4_na_dbEST.same.dmel sim4_na_dbEST.diff.dmel 
glyph         = segments
strand_arrow  = 1
bgcolor       = lightgreen
fgcolor       = green
bump          = 1
key           = EST 
category = "Genome reagents and data"
label = sub { my $f = shift; 
	(my $name) = $f->{'ftname'}; 
	my $v=$f->{'gff_string'}; 
	if( $v=~/Target=([^ \t;]+)[ \t;]/ ) { $name= $1; }  
	return $name; 
	}
link = sub { my $f = shift;
	my $v=$f->{'gff_string'}; 
	if( $v=~/Target=([^ \t;]+)[ \t;]/ ) {   
  	return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$1; }
	return("");  
  }

[oligo_1]
feature  = dmel_r3_to_dmel_r4_migration_dmel_r3_affy_oligos
glyph         = generic
strand_arrow  = 1
bgcolor       = tomato
fgcolor       = tomato
height       = 4
key           = Affymetrix v1
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = 
 
[oligo_2]
feature  = oligonucleotide:Drosophila_2
glyph         = generic
strand_arrow  = 1
bgcolor       = tomato
fgcolor       = tomato
height       = 4
key           = Affymetrix v2
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = 
 
[pcr_product_1]
feature  = pcr_product:DGRC_1
glyph         = generic
bgcolor       = tomato
fgcolor       = tomato
height       = 4
key           = DGRC-1 amplicons
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = 
 
[oligo_3]
feature  = oligonucleotide:DGRC_2
glyph         = generic
strand_arrow  = 1
bgcolor       = tomato
fgcolor       = tomato
height       = 4
key           = DGRC-2 oligos
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = 
 
[pcr_product_2]
feature  = pcr_product:DRSC
glyph         = generic
bgcolor       = tomato
fgcolor       = tomato
height       = 4
key           = DRSC RNAi amplicons
category = "Genome reagents and data"
label = sub { my $f = shift;
	(my $name) = $f->{'ftname'}; 
	my $v= $f->{'dbxref'}; 
	if( $v=~/DRSC:(DRSC\d+)/ ) { $name= $1; }  
	return($name); 
	}
link = sub { my $f = shift;
	my $v= $f->{'dbxref'}; 
	if( $v=~/DRSC:(DRSC\d+)/ ) {
		$f->{'ftname'}= $1;   
  	return 'http://teratogen.med.harvard.edu/cgi-bin/RNAi_gene_lookup_public.pl?gname='.$1; }
	return("");  
  }
 
[BAC_1]
feature  = BAC_cloned_genomic_insert
glyph         = extending_arrow
no_arrows     = 1
base          = 0
bgcolor       = lightslategray
fgcolor       = lightslategray
linewidth     = 2
bump          = 1
key           = Tiling BAC
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = 

[proteomic_1]
feature   = blastp_Dmel_proteomic
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = Proteomic analysis 
category = "Genome reagents and data"
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; 
	if($name=~/^proteomic_([^_]+)_/) { return($1); } else { return $name; } }
link = 

#-------- Mapped features -------------------

[protein_binding_site_1]
feature  = protein_binding_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = protein_binding_site 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[rescue_fragment]
feature  = rescue_fragment
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = rescue fragment 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[enhancer]
feature  = enhancer
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = enhancer 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[transposable_element_target_site_duplication]
feature  = transposable_element_target_site_duplication
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = transposable element target site duplication 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[regulatory_region]
feature  = regulatory_region
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = regulatory region 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[point_mutation]
feature  = point_mutation
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = point_mutation 
category = "Mapped features"
key = Mutation: point mutation
label = sub { my $f = shift; (my $name) = $f->{'ftname'}; return $name; }
link = sub { 
	my $f = shift; my $v= $f->{'dbxref'};  
	if( $v=~/(FBal\d+)/ ) { return('/cgi-bin/fbidq.html?'.$1); }
	else { return "javascript:void(0)"; } 
  }
  
[sequence_variant]
feature  = sequence_variant
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: sequence variant
category = "Mapped features"
link = sub { 
	my $f = shift; my $v= $f->{'id'}; return('/cgi-bin/fbaleq.html?symbol='.$v); 
  }

[uncharacterized_change_in_nucleotide_sequence]
feature  = uncharacterized_change_in_nucleotide_sequence
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: uncharacterized change in nucleotide_sequence 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[aberration_junction]
feature  = aberration_junction
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: aberration junction 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[complex_substitution]
feature  = complex_substitution
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: complex substitution 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[deletion]
feature  = deletion
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: deletion 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

[insertion_site]
feature  = insertion_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = Mutation: insertion site 
category = "Mapped features"
label = sub { my $f = shift; (my $name) = $f->{'id'}; return $name; }
link = 

#-------- Analysis -------------------

[transcription_start_site_1]
feature  = match:transcription_start_site match:promoter
glyph         = anchored_arrow
bgcolor       = purple
fgcolor       = purple
bump          = 1
key = Promoter prediction
category = "Prediction features"
label = 0
link = 

[repeat_region_1]
feature   = repeat_region match:repeat_runner_seg match:repeatmasker_dummy match:Tandem_Repeat_Finder_75-20
# glyph         = extending_arrow
bgcolor       = darkorchid
fgcolor       = darkorchid
height        = 3
connector     = solid
bump          = 1
strand_arrow  = 0
key           = Repeat region
category = "Prediction features"
label = 0
link = 

[augustus_1]
feature   = augustus
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
key           = Augustus prediction
category = "Prediction features"
label = 0
link = 

[genscan_1]
feature   = genscan_masked
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
key           = Genscan prediction
category = "Prediction features"
label = 0
link = 

[genie_1]
feature   = genie_masked
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = Genie prediction 
category = "Prediction features"
label = 0
link = 

[geneid_1]
feature   = RGUI_geneid_v1.2 RGUI_geneid_v1.2_u12
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = GeneID prediction 
category = "Prediction features"
label = 0
link = 

[HDP_1]
feature = sim4_na_HDP_mRNA.dmel 
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           =HDP prediction 
category = "Prediction features"
label = 0
link = 

[RNAiHDP_1]
feature = sim4_na_HDP_RNAi.dmel
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
key           = RNAiHDP prediction 
category = "Prediction features"
label = 0
link = 

[tRNAscan_SE_1]
feature   = tRNAscan-SE
glyph = transcript2
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = tRNAscan prediction
citation     = tRNAscan (tRNA prediction) 
category = "Prediction features"
label = 0
link = 

[NCBI_gnomon_1]
feature   = NCBI_gnomon
glyph = transcript2
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = NCBI gnomon prediction
citation     = NCBI_gnomon  
category = "Prediction features"
label = 0
link = 

[CONTRAST_1]
feature   = BATZ_Contrast BATZ_Contrast_NA
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = CONTRAST prediction 
category = "Prediction features"
label = 0
link = 

[SNAP_1]
feature   = DGIL_snap DGIL_snap_homology
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = SNAP prediction 
category = "Prediction features"
label = 0
link = 

[CONGO_1]
feature   = CONGO
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
key           = CONGO exons 
category = "Prediction features"
label = 0
link = 

#---------- Similarity: Proteins --------------

[blastx_dmel_1]
feature  = blastx_masked_aa_SPTR.dmel prosplign_aa_ncbi_dmel
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = D melanogaster protein
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }
  
[blastx_insect_1]
feature  = blastx_masked_aa_SPTR.insect
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Other Insect proteins
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_worm_1]
feature  = blastx_masked_aa_SPTR.worm
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Worm protein 
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_yeast_1]
feature  = blastx_masked_aa_SPTR.yeast
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Yeast protein 
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_othinv_1]
feature  = blastx_masked_aa_SPTR.othinv
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Other invert. protein
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_primate_1]
feature  = blastx_masked_aa_SPTR.primate
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Primate protein 
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_othvert_1]
feature  = blastx_masked_aa_SPTR.rodent blastx_masked_aa_SPTR.othvert
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Vertebrate protein 
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[blastx_plant_1]
feature  = blastx_masked_aa_SPTR.plant
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Plant protein 
category = "Similarity: Proteins"
label = 0
link = sub { my $ac=shift->{'id'}; $ac=~s/[:.].*$//;  
  if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
  elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
  }

[prosplign_other_1]
feature   = prosplign_aa_ncbi_other
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key           = other proteins 
citation     = other proteins 
category = "Similarity: Proteins"
label = 0
link = 

#-------- Similarity: Translated nucleotides ---------

[tblastx_dpse_1]
feature  = tblastxwrap_masked_na_baylorf1_scfchunk.dpse
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
link     = AUTO
key      = D pseudoobscura contigs
category = "Similarity: Translated nucleotides"
label = 0
link = 

[tblastx_insect_1]
feature  = tblastx_masked_na_dbEST.insect
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Insect dbEST 
category = "Similarity: Translated nucleotides"
label = 0
link = sub { my $v=shift->{'id'};  $v=~s/[:.].*(prime|contig).*$//;  $v=~s/^(GB)[:]//;  
  return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;  
  }

[tblastx_agambiae_1]
feature  = tblastxwrap_masked_na_scf_chunk_agambiae.fa
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = Mosquito NA 
category = "Similarity: Translated nucleotides"
label = 0
link = sub { my $v=shift->{'id'};  $v=~s/^(GB)[:]//;  $v=~s/[:.].*$//; 
  return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;  
  }

#-------- Prior annotations ---------

[sim4_transcript_dmel_r32_1]
feature  = sim4_na_transcript.dmel.RELEASE32
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key = Dmel r32 transcript
category = "Prior annotations"
label = 0
link = 

[sim4_transcript_dmel_r31_1]
feature  = sim4_na_transcript.dmel.RELEASE31
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key = Dmel r31 transcript
category = "Prior annotations"
label = 0
link = 

[sim4_gadfly_dmel_r2_1]
feature  = sim4_na_re2.dros sim4_na_gadfly.dros.RELEASE2
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key = Dmel r2 transcript
category = "Prior annotations"
label = 0
link = 

[sim4_smallRNA_dros_1]
feature  = sim4_na_smallRNA.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key =  Dros smallRNA
category = "Prior annotations"
label = 0
link = 

[sim4_ARGs_dros_1]
feature  = sim4_na_ARGs.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key = Dmel ARGs
category = "Prior annotations"
label = 0
link = 

[sim4_ARGsCDS_dros_1]
feature  = sim4_na_ARGsCDS.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key = Dmel ARGs CDS
category = "Prior annotations"
label = 0
link =