[GENERAL]
description = S. cerevisiae chromosome I
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-dir $ENV{GBROWSE_DOCS}/sample_data/
aggregators = transcript alignment orf
plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest
# where to link to when user clicks in detailed view
link = AUTO
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
default features = Genes
ORFs
tRNAs
Centro:overview
# 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
reference class = Sequence
# max and default segment sizes for detailed view
max segment = 500000
default segment = 50000
# zoom levels
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources = 1
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
# examples to show in the introduction
examples = I
I:80,000..120,000
"membrane trafficking"
NUT21
ORF:YAL063C
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
label density = 25
bump density = 100
########################
# database configuration
########################
[yeast1:database]
db_args = -adaptor memory
-dir $ENV{GBROWSE_DOCS}/sample_data/
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[Centro:overview]
feature = CEN:sgd
bgcolor = blue
glyph = dot
fgcolor = black
height = 8
point = 1
key = Centromeres
[Genes]
feature = gene:sgd
data source = sgd
track source = modENCODE
glyph = generic
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height = 6
description = 1
key = Named gene
[ORFs]
feature = ORF:sgd
glyph = arrow
fgcolor = red
data source = sgd
track source = "nicole washington" modENCODE
linewidth = 2
height = 6
description = 1
key = ORF
[CDS]
feature = ORF:sgd
glyph = cds
description = 0
height = 26
data source = sgd flybase
track source = "Marc Perry" modENCODE
# we need this because the yeast GFF file does not define the phase
allow_empty_phase = 1
sixframe = 1
label = CDS frame
key = CDS
citation = This track shows CDS reading frames.
[tRNAs]
feature = tRNA:sgd
glyph = generic
bgcolor = lightgray
fgcolor = black
height = 4
stranded = 1
description = 1
key = tRNAs
[Transp]
feature = Transposon:sgd
glyph = segments
bgcolor = yellow
fgcolor = black
height = 5
stranded = 1
key = Transposons
[LTRs]
feature = LTR:sgd
fgcolor = black
glyph = anchored_arrow
height = 6
key = Long Terminal Repeats
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
strand = +1
translation = 6frame
key = 6-frame translation
[TranslationF]
glyph = translation
global feature = 1
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
strand = both
fgcolor = red
axis_color = blue
[TranslationR]
glyph = translation
global feature = 1
height = 20
fgcolor = blue
strand = -1
translation = 3frame
key = 3-frame translation (reverse)
[ncRNA]
feature = RNA:sgd rRNA:sgd snRNA:sgd snoRNA:sgd
fgcolor = orange
glyph = generic
description = 1
key = Noncoding RNAs