# gbrowse config file for flybase gene maps
# d.gilbert, aug02
# set for use in flybase portable server (all paths and urls are relative)
## WARNING - gbrowse plumbing is now doing lc(key) on all config keys !
[GENERAL]
description = D. melanogaster Genome (R3.2.2)
organism = D. melanogaster
#datapath = /data2/fban/gnomap
datapath = /genomes/Drosophila_melanogaster/dmel_r3.2.2_10212004/gnomap
# synteny tests; 04oct
synteny_idmap = dpse-synt-idmap.tsv
synteny_org = D. pseudoobscura
synteny_src = dpse
header =
FlyBase Genome Browser: D. melanogaster Release 3.2.2; Oct 2004
footer =
Adapted from GBrowse of the
Generic Model Organism Database Project.
## expects adaptor to be subclass of Bio/DB/GFF/Adaptor/
adaptor = flybase::gmod::FFFdb
default_name = X:100000-200000
default_range = 1-500000
# examples to show in the introduction
examples =
X: 2L: 2R: 3L: 3R: 4:
X:8270000..8470000
2L:3500000..3800000
FBgn0000014 FBgn0019650
chromosomes =
X: 2L: 2R: 3L: 3R: 4:
searchhelp =
#Search using Chromosome:base_start..end or FlyBase Gene ID.
## -- revise search methods; call searchsub from gbrowse instead of javascript
# chipmunk% $f/cgi-bin/fbannq2map -h xfieldname1=symbol name=toy
# Status: 302 Found
# Location: gbrowse_fb?id=FBgn0019650
## -- for multiple matches, need to use gbrowse overview function
# call searchsub(funct,kinase)
# searchsub: /bio/biodb/flybase/web/../cgi-bin/fbannq2map -Dh 'xfieldname1=funct' 'name=kinase'
# DEBUG getHTTPin: q=xfieldname1=funct name=kinase=
# DoSRSAcodeQuery: /bio/biodb/flybase/web/.srs/bin/macosx/asksrs -P acode -odir /bio/biodb
# /flybase/web/tmp/fban2378.data ' [FBan-pro:*kinase*] '
# query_to_map: [FBan-pro:*kinase*] , /bio/biodb/flybase/web/tmp/fban2378.data n=367
# putResultsList count= 367
# printResultList: path=/bio/biodb/flybase/web/tmp data=fban2378.data start=1 content=
# nrecords= 367
searchsub = sub {
my ($fld,$val)= @_;
if ($fld && $fld !~ m/^(name|ref|id|cytoloc)/) {
my $cgi ="$ENV{DOCUMENT_ROOT}/../cgi-bin/fbannq2map"; # FIXME
my $call="$cgi -h 'xfieldname1=$fld' 'name=$val'"; # -D = debug
$ENV{'REQUEST_METHOD'}='GET'; # stupid cgi fix
warn "searchsub: $call\n";# if DEBUG;
my $res = `$call`;
## warn "searchsub: res=$res; err=$@\n";# if DEBUG;
if ($res =~ m/id=(\w+)/s) { ($fld,$val)=('id',$1); }
elsif ($res =~ m/name=([^;,\s]+)/s) { ($fld,$val)=('name',$1);}
}
return($fld,$val);
}
searchitem = Find
\n
\n
\n
# OLDsearchtop =
#
# OLDsearchitem = Find
# \n
# \n
# \n
#
plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper
# GFFDumper - not as good as BatchDumper
# OligoFinder - requires Bio::DB::GFF sql calls
uploads = 1
default features = rev_ruler cytoband gene tRNA noncodingRNA pseudogene
syntenic_region scaffold BAC transposable_element
primary_feature = gene
secondary_feature = mRNA intron five_prime_UTR three_prime_UTR
scale_feature = cytoband
# ignore these for now - NO?
# feature_skip = cytoabs cytodef cytodup cytogene cytoins cytoinv cytotloc cytowalk
dumpviews = FastA GenBank GFF FFF
# dumpviews =
dataviews = "Default" "Collapse All" "Expand All"
# "Labelling On"
# Web site configuration info
# stylesheet = /templates/gbrowse.css
# help = /maps/gbrowse
help = /common/perl/gbrowse_fb/htdocs
stylesheet = /common/perl/gbrowse_fb/gbrowse.css
buttons = /common/perl/gbrowse_fb/images/buttons
tmpimages = /tmp/gbrowse_fb
bac_insitu_pic = /images/lk/bac_insitu_pic
# max num bac image display (set to 0 to disable)
max bac pic = 3
# 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 = 60000
expand_by = 20000
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
#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
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 '' ; }
# fbanlink = sub {
# my $f= shift;
# my $d= $f->primary_id() if $f->can('primary_id');
# $d= $f->source() unless($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()) { my $v=$f->name(); $v=~s/\+/?/g; return '/cgi-bin/fbannq.html?synonym='.$v; }
# return '' ; }
# title = sub { my $f=shift; return ($f->name())? $f->name(): "" ; }
# make_title in Browser should be doing this, but get only "Gene" == class?
## the perl syntax ->method||'' was causing failure !
title = sub { my $f= shift;
return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
}
# link.ID.euGenes = http://eugenes.org/.bin/moidq.html?
# link.ID.FlyBase = http://flybase.net/.bin/fbidq.html?
# link.ID.GadFly = http://flybase.net/cgi-bin/fbannq.html?synonym=
dbx_link = sub {
my $dbx= shift; my $f= shift; #?
my $r='';
foreach my $x (split(/[,;]\s*/,$dbx)) {
my($h,$v);
my($db,$ac)= split/:/,$x,2;
if ($x =~ /(FB\w\w\d+)/) { $v=$1; $h= '/cgi-bin/fbidq.html?'.$v; }
elsif ($db =~ /FlyBase/i) { $v=$ac; $h= '/cgi-bin/fbsymq.html?'.$ac; }
elsif ($db eq 'GB_protein') {
$v= $ac;
$h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenBank&tool=FlyBase&term='.$ac;
}
elsif ($db eq 'GB') {
$v= $ac;
$h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$ac;
}
elsif ($db eq 'GO') {
$v= $ac;
$h= '/cgi-bin/goreport?id='.$ac;
}
if ($h && $v) { $r.= ''.$v.', '; }
else { $r.= $x.', '; }
}
return $r;
}
# "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 of detailed view (pixels)
default width = 800
width = 800
#---------- end [GENERAL] ------------------------
# NOTE: Ordering here is Bottom -> Up (or Center -> Up/Down)
# rev_ruler/cytoband is center ruler
# bperl equates [label] with feature type
[rev_ruler]
glyph = ruler_arrow
#glyph = revcomp_arrow
label = 0
no_53_label = 1
label_align = center
tick = 1
no_tick_label = 0
units = K
link =
key = Base ruler
nodump = 1
keygroup = " Genomic features"
# keygroup = "hidden"
#-------- Genomic features -------------------
[cytoband]
feature = cytoband
glyph = revcomp_arrow
nodump = 1
both = 1
label_align = center
fgcolor = black
bgcolor = black
linewidth = 2
label = 1
label density = 10000
bump = 0
bump density = 0
key = Cytologic band
keygroup = " Genomic features"
citation = Cytological bands on the polytene chromosomes
link = sub { my $f=shift; my $u=$ENV{REQUEST_URI};
my $r= $f->ref.":".$f->to_FTstring;
$u =~ s/\?.*$//; $u .= '?name='.$r.";doexpand=1";
return $u;
}
# options = 1
# title = sub { shift->name(); }
# description = Cytologic band
[dna]
feature = source
glyph = dnabases
draw_dna = 1
nodump = 1
strand = forward
label = 0
label density = 0
key = DNA sequence
keygroup = " Genomic 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
bump density = 150
# height = 6
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 '' ; }
#------ GM SUBS
[genespan]
feature = gene
glyph = transcript2
bgcolor = lightblue
fgcolor = blue
highlight_color = red
higlighted = 1
label = 1
label density = 50
bump density = 150
key = Gene span
keygroup = " Gene Model subfeatures"
citation = Gene span 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 '' ; }
[mRNA]
feature = mRNA
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = 1
key = mRNA
citation = Protein coding sequence (CDS or translation; annotation DB ; Chado)
keygroup = " Gene Model subfeatures"
link =
[CDS]
feature = CDS
# glyph = translation
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 = " Gene Model subfeatures"
link =
[intron]
feature = intron
glyph = segments
stranded = 1
label = 1
key = intron
citation = intron
keygroup = " Gene Model subfeatures"
link =
[five_prime_UTR]
feature = five_prime_UTR
glyph = segments
stranded = 1
label = 1
key = 5prime UTR
citation = five_prime_UTR
keygroup = " Gene Model subfeatures"
link =
[three_prime_UTR]
feature = three_prime_UTR
glyph = segments
stranded = 1
label = 1
key = 3prime UTR
citation = three_prime_UTR
keygroup = " Gene Model subfeatures"
link =
[pseudogene]
feature = pseudogene
glyph = segments
strand_arrow = 1
#glyph = anchored_arrow
fgcolor = orange
label = 1
key = Pseudogene
keygroup = " Genomic features"
[tRNA]
feature = tRNA
glyph = transcript2
label = 1
#strand_arrow = 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.
[noncodingRNA]
feature = ncRNA snoRNA snRNA miscRNA
glyph = transcript2
bgcolor = peachpuff
#strand_arrow = 1
stranded = 1
key = Non-coding RNAs
citation = Non-coding RNAs: ncRNA snoRNA snRNA miscRNA
keygroup = " Genomic features"
[transposable_element]
feature = transposable_element
# fgcolor = violet
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"
# 04oct test only; is this same as above? can we drop it?
# same as transposable_element_pred ?
# [pinsertion]
# feature = pinsertion
# glyph = pinsertion
# bgcolor = lightslategray
# fgcolor = black
# key = pinsertion
# citation = pinsertion
# keygroup = "Analysis features"
# link =
#-------- Misc. Genomic features -------------------
[polyA_site]
feature = polyA_site
#glyph = segments
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;
}
#my $d= $f->primary_id() if $f->can('primary_id');
#$d= $f->source() unless($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 =~/\S/) { return '/cgi-bin/fbannq.html?'.$d; }
# Gsc-polyA_site-585205..585205 2L
[point_mutation]
feature = point_mutation
# glyph = segments
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
# glyph = segments
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;
}
[rescue_fragment]
feature = rescue_fragment
# glyph = segments
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;
}
[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;
}
[signal_peptide]
feature = signal_peptide
glyph = segments
strand_arrow = 1
bgcolor = palegoldenrod
fgcolor = orange
label = 1
key = signal_peptide
citation = signal_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;
}
[enhancer]
feature = enhancer
# glyph = segments
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;
}
[aberration_junction]
feature = aberration_junction
# glyph = segments
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;
}
# add: regulatory_region and sequence_variant
[regulatory_region]
feature = regulatory_region
# glyph = segments
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;
}
[sequence_variant]
feature = sequence_variant
# glyph = segments
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;
}
[DNA_motif]
feature = DNA_motif RNA_motif
# glyph = segments
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"
# disabled 6/23/04 on Kathy's advice - they are pre-historic FB curations
# [insertion_site]
# feature = insertion_site
# # glyph = segments
# bgcolor = lightslategray
# fgcolor = lightslategray
# key = insertion_site
# citation = insertion_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;
# }
# link = sub {
# my $f= shift;
# my $d= $f->primary_id() if $f->can('primary_id');
# $d= $f->source() unless($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 =~/\S/) { return '/cgi-bin/fbannq.html?'.$d; }
# if ($f->name()) { return '/cgi-bin/fbannq.html?'.$f->name(); }
# }
#-------- Synteny -------------------
# [orthologous_region]
# feature = orthologous_region
# glyph = anchored_arrow
# no_arrows = 1
# bgcolor = palegoldenrod
# fgcolor = turquoise
# label = 1
# key = Ortholog
# citation = Orthologous_region
# keygroup = " Synteny features"
# link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } }
[orthologous_region]
feature = orthologous_region
glyph = transcript2
bgcolor = palegoldenrod
fgcolor = turquoise
label = 1
label density = 50
height = 4
key = Ortholog
citation = Orthologous_region
keygroup = " Synteny features"
link = sub { my $f= shift;
my ($id)= $f->each_tag_value('id');
unless ($id) { my $nm= $f->name(); $id= $nm if ($nm=~/^ortho:/); }
if ($id) { return '?syn='.$id; }
}
# rename = sub { my $f= shift; my $tn= '';
# my ($nt)= $f->each_tag_value('note');
# if ($nt =~ m/to_species=([^;,]+)/) { $tn .= $1.'\\'; }
# if ($nt =~ m/to_name=([^;,]+)/) { $tn .= $1; }
# $tn ||= $f->info;
# return $tn;
# }
[syntenic_region]
feature = syntenic_region
glyph = segments
bgcolor = pink
fgcolor = darkred
label = 1
key = Syntenic region
citation = Syntenic_region
keygroup = " Synteny features"
link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } }
#-------- Analysis -------------------
[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"
#key = Transcription start
[processed_transcript]
feature = processed_transcript
glyph = processed_transcript
bgcolor = plum
fgcolor = plum
height = 4
bump = 1
label = 0
key = Processed transcript
citation = processed_transcript (annotation DB ; Chado)
keygroup = "Analysis features"
[protein]
feature = protein
# glyph = segments
bgcolor = salmon
fgcolor = salmon
height = 3
strand_arrow = 1
bump = 1
label = 1
key = Protein BLAST alignment
citation = protein from BLAST alignments (annotation DB ; Chado)
keygroup = "Analysis 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 =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
}
if ($f->name() =~ /^(\w+):(\w+)/){ return '/cgi-bin/fbannq.html?DBX='.$f->name; }
return '' ; }
#above DBX should go to swissprot et al web db
[repeat_region]
feature = repeat_region
# glyph = extending_arrow
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 =
[mRNA_genscan]
feature = mRNA_genscan
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = Genscan prediction
citation = Genscan (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[mRNA_piecegenie]
feature = mRNA_piecegenie
glyph = segments
strand_arrow = 1
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key = Genie prediction
citation = PieceGenie (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[match_fgenesh]
feature = match:fgenesh
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = fgenesh prediction
citation = match_fgenesh (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[match_HDP]
feature = match:HDP
glyph = segments
strand_arrow = 1
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key =HDP prediction
citation = HDP (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[match_RNAiHDP]
feature = match:RNAiHDP
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = RNAiHDP prediction
citation = RNAiHDP (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[tRNA_trnascan]
feature = tRNA:trnascan
glyph = transcript2
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key = tRNAscan prediction
citation = tRNAscan (tRNA prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
link =
[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 =
#------- various analyses added r3.2.2 ------
[m_promoter]
feature = match:promoter
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = promoter
citation = promoter
keygroup = "Analysis features"
[m_repeat_runner_seg]
feature = match:repeat_runner_seg
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = repeat_runner_seg
citation = repeat_runner_seg
keygroup = "Analysis features"
[m_repeatmasker]
feature = match:repeatmasker
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = repeatmasker
citation = repeatmasker
keygroup = "Analysis features"
[mb_aaSPhypdros]
feature = match:blastx_masked:aa_SP.hyp.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SP.hyp.dros
citation = blastx:aa_SP.hyp.dros
keygroup = "Blast features"
link =
[mb_aaSPrealdros]
feature = match:blastx_masked:aa_SP.real.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SP.real.dros
citation = blastx:aa_SP.real.dros
keygroup = "Blast features"
link =
[mb_aaSPTRdros]
feature = match:blastx_masked:aa_SPTR.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.dros
citation = blastx:aa_SPTR.dros
keygroup = "Blast features"citation = blastx:aa_SPTR.dros
keygroup = "Blast features"
link =
[mb_aaSPTRinsect]
feature = match:blastx_masked:aa_SPTR.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.insect
citation = blastx:aa_SPTR.insect
keygroup = "Blast features"
link =
[mb_aaSPTRothinv]
feature = match:blastx_masked:aa_SPTR.othinv
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.othinv
citation = blastx:aa_SPTR.othinv
keygroup = "Blast features"
link =
[mb_aaSPTRothvert]
feature = match:blastx_masked:aa_SPTR.othvert
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.othvert
citation = blastx:aa_SPTR.othvert
keygroup = "Blast features"
link =
[mb_aaSPTRplant]
feature = match:blastx_masked:aa_SPTR.plant
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.plant
citation = blastx:aa_SPTR.plant
keygroup = "Blast features"
link =
[mb_aaSPTRprimate]
feature = match:blastx_masked:aa_SPTR.primate
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.primate
citation = blastx:aa_SPTR.primate
keygroup = "Blast features"
link =
[mb_aaSPTRrodent]
feature = match:blastx_masked:aa_SPTR.rodent
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.rodent
citation = blastx:aa_SPTR.rodent
keygroup = "Blast features"
link =
[mb_aaSPTRworm]
feature = match:blastx_masked:aa_SPTR.worm
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.worm
citation = blastx:aa_SPTR.worm
keygroup = "Blast features"
link =
[mb_aaSPTRyeast]
feature = match:blastx_masked:aa_SPTR.yeast
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_SPTR.yeast
citation = blastx:aa_SPTR.yeast
keygroup = "Blast features"
link =
[mb_aaTRrealdros]
feature = match:blastx:aa_TR.real.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = blastx:aa_TR.real.dros
citation = blastx:aa_TR.real.dros
keygroup = "Blast features"
link =
[mt_nadbESTinsect]
feature = match:tblastx:na_dbEST.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = tblastx:na_dbEST.insect
citation = tblastx:na_dbEST.insect
keygroup = "Blast features"
link =
[mt_naunigenerodent]
feature = match:tblastx:na_unigene.rodent
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = tblastx:na_unigene.rodent
citation = tblastx:na_unigene.rodent
keygroup = "Blast features"
link =
[ms_naDGCdros]
feature = match:sim4:na_DGC.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_DGC.dros
citation = sim4:na_DGC.dros
keygroup = "sim4 features"
link =
[ms_naESTall_nrdros]
feature = match:sim4:na_EST.all_nr.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_EST.all_nr.dros
citation = sim4:na_EST.all_nr.dros
keygroup = "sim4 features"
link =
[ms_nacDNAdros]
feature = match:sim4:na_cDNA.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_cDNA.dros
citation = sim4:na_cDNA.dros
keygroup = "sim4 features"
link =
[ms_nagadflydrosRELEASE2]
feature = match:sim4:na_gadfly.dros.RELEASE2
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_gadfly.dros.RELEASE2
citation = sim4:na_gadfly.dros.RELEASE2
keygroup = "sim4 features"
link =
[ms_nagbdros]
feature = match:sim4:na_gb.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_gb.dros
citation = sim4:na_gb.dros
keygroup = "sim4 features"
link =
[ms_napedros]
feature = match:sim4:na_pe.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = sim4:na_pe.dros
citation = sim4:na_pe.dros
keygroup = "sim4 features"
link =
#-------- Genome reagents -------------------
## was oligonucleotide; SO term = oligo now
[oligo]
feature = oligo
#glyph = triangle
glyph = generic
bgcolor = tomato
fgcolor = tomato
height = 4
bump = 0
bump density = 1
label = 0
label density = 0
key = Affy Oligo
citation = oligonucleotide (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
return ($f->name())?'/cgi-bin/fbannq.html?oligo='.$f->name() : ''; }
## FIXME: feat types renamed
# ^ EST (310718) becomes
# match_sim4_na_EST.all_nr.dros (267828) ms_naESTall_nrdros
# + match_sim4_na_DGC.dros (15270) + ?? ms_naDGCdros
# cDNA_clone (10283) becomes match_sim4_na_cDNA.dros (10319) ms_nacDNAdros
[EST]
feature = EST cDNA_clone
glyph = segments
strand_arrow = 1
bgcolor = lightgreen
fgcolor = green
secondary = cDNA_clone
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
key = cDNA + EST
citation = cDNA_clone and EST (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub {
my $v=shift->name(); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//;
return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;
}
#drop from link name: .5prime_revcomp .5prime, :contig1, SD02026:contig1, CK02552.5prime
# but for ones like GB:AV399447 drop db:
#link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term=$info
#link = http://www.fruitfly.org/cgi-bin/EST/community_query/ctgReport.pl?db=estlabtrack&id_type=0&id_value=$info
# keep here so shows at top near BAC track
[blast]
feature = blast
glyph = alignment
bgcolor = darkorchid
fgcolor = darkorchid
bump = 1
label = 1
key = Blast hit
height = 8
citation = BLAST alignment hit
keygroup = "hidden"
link =
[BAC]
feature = BAC
glyph = extending_arrow
no_arrows = 1
#west = 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() : ''; }
## aug04 - was segment; renamed to SO equivalent golden_path ???
[scaffold]
feature = golden_path scaffold
glyph = anchored_arrow
# anchored_arrow
no_arrows = 1
#northeast = 1
base = 0
fgcolor = black
bgcolor = black
linewidth = 2
bump = 1
label = 1
# relative_coords = 1
height = 4
key = GenBank Scaffold
citation = golden_path segment (annotation DB ; Chado)
keygroup = " Genome reagents"
#key = GenBank unit
link = sub { my $f= shift;
return ($f->name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; }
#----------- Cytology mapped ----------------
# New aberration classes from Kathy
[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"
[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"
[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_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"
[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"
[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"
#---------------------------------------