[GENERAL]
description = Yeast chromosomes 1+2 (advanced)
database = scaffolds
initial landmark = chrI:143000..180000
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1
default tracks = Genes
ORFs
tRNAs
CDS
Transp
Centro:overview
GC:region
# examples to show in the introduction
examples = chrI
chrII
chrI:80,000..120,000
"membrane trafficking"
NUT21
YAL063C
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir $DATABASES/yeast_scaffolds
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir $DATABASES/yeast_chr1+2
search options = default +autocomplete
# Advanced feature: custom balloons
custom balloons = [balloon]
delayTime = 500
[balloon500]
maxWidth = 500
delayTime = 50
# Advanced feature: an example of callbacks to be run remotely
# by gbrowse_details for AJAX/iframe balloons
[TOOLTIPS]
intro = sub {
my $args = shift;
my $feat = $args->{feature};
my $name = $feat->display_name;
my $type = $feat->primary_tag;
my $class = $feat->class;
my $extra = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
my $n = $type =~ /^[AEIOU]/i ? 'n' : '';
my $msg = "Hello, I am $name, a$n $type of class $class";
$msg .= "<br>I am described as a <i><b>$extra</b></i>" if $extra;
$msg .= "<br>Click to see the sequence of $name";
return "<table><tr><th bgcolor='lightsteelblue'>$name</th><tr>" .
"<tr><td>$msg</td></tr></table>";
}
full_sequence = sub {
my $args = shift;
my $feat = $args->{feature};
my $name = $feat->display_name;
my $seq = $feat->seq->seq;
$seq =~ s/(\S{75})/$1\n/g;
return "<pre style='font-size:8pt'>>$name\n$seq</pre>";
}
# Advanced feature:
# Pop up rubberband menus for submitting selected region to search engines...
#include "detail_select_menu.conf"
#include "submitter_plugin.conf"
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
# default pop-up balloon
balloon hover = <b>$name</b> is a $type spanning $ref from $start to $end. Click for more details.
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[Centro:overview]
feature = centromere
bgcolor = blue
glyph = dot
fgcolor = black
height = 8
point = 1
show summary = 0 # no summary of this one
key = Centromeres
[tRNA:overview]
feature = tRNA
glyph = generic
bgcolor = lightgray
fgcolor = black
height = 4
stranded = 1
description = 1
show summary = 0 # no summary of this one
key = tRNAs
[GC:region]
glyph = dna
global feature = 1
database = scaffolds
height = 40
gc_window = auto
do_gc = 1
strand = both
fgcolor = red
axis_color = blue
show summary = 0 # no summary of this one
key = GC Content
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
label = sub { my $f = shift;
my $name = $f->display_name;
my @aliases = sort $f->attributes('Alias');
$name .= " (@aliases)" if @aliases;
$name;
}
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my $f = shift; return join ' ',$f->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><img src='http://www.yeastgenome.org/images/SGD_logo.gif'/><br>
This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
<th bgcolor="cyan">Gene $name</th>
</tr>
<tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast_advanced?feature_id=$id" target="_new">See gene details</a></th></tr>
<tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
<tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
<tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
</table>
key = Named gene
[CDS]
feature = gene
glyph = cds
description = 0
height = 26
sixframe = 1
label = sub {shift->name . " reading frame"}
key = CDS
balloon click width = 500
balloon hover width = 350
balloon hover = <b>$name</b> is a $type spanning $ref from $start to $end. Click to search Google for $name.
balloon click = http://www.google.com/search?q=$name
citation = This track shows CDS reading frames.
[tRNAs]
feature = tRNA
glyph = generic
bgcolor = lightgray
fgcolor = black
height = 4
stranded = 1
description = 1
# Note: AJAX balloons -- edit the URL if your copy of gbrowse_details is not in /gb2
balloon hover = url:../../gbrowse_details/yeast_advanced?name=$name;class=$class;remote=intro
balloon click = url:../../gbrowse_details/yeast_advanced?name=$name;class=$class;remote=full_sequence
key = tRNAs
[Transp]
feature = LTR_retrotransposon
glyph = segments
bgcolor = yellow
fgcolor = black
height = 5
stranded = 1
balloon width = 375
key = Transposons
[LTRs]
feature = long_terminal_repeat
fgcolor = black
glyph = anchored_arrow
height = 6
balloon width = 375
key = Long Terminal Repeats
[Translation]
glyph = translation
global feature = 1
database = scaffolds
height = 40
fgcolor = purple
strand = +1
translation = 6frame
key = 6-frame translation
[TranslationF]
glyph = translation
global feature = 1
database = scaffolds
height = 20
fgcolor = purple
strand = +1
translation = 3frame
key = 3-frame translation (forward)
[DNA/GC Content]
glyph = dna
global feature = 1
database = scaffolds
height = 40
do_gc = 1
gc_window = auto
strand = both
fgcolor = red
axis_color = blue
[TranslationR]
glyph = translation
global feature = 1
database = scaffolds
height = 20
fgcolor = blue
strand = -1
translation = 3frame
key = 3-frame translation (reverse)
[ncRNA]
feature = RNAd rRNA:sgd snRNA:sgd snoRNA:sgd
fgcolor = orange
glyph = generic
description = 1
key = Noncoding RNAs