[GENERAL]
description = Yeast chromosomes 1+2 (basic)
database = scaffolds
initial landmark = chrI:143000..180000
plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper
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
# 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
### 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 = gene
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
key = Named gene
[CDS]
feature = gene
glyph = cds
description = 0
height = 26
sixframe = 1
label = sub {shift->name . " reading frame"}
key = CDS
citation = This track shows CDS reading frames.
[tRNAs]
feature = tRNA
glyph = generic
bgcolor = lightgray
fgcolor = black
height = 4
stranded = 1
description = 1
key = tRNAs
[Transp]
feature = LTR_retrotransposon
glyph = segments
bgcolor = yellow
fgcolor = black
height = 5
stranded = 1
key = Transposons
[LTRs]
feature = long_terminal_repeat
fgcolor = black
glyph = anchored_arrow
height = 6
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