[GENERAL]
description = S. cerevisiae (via SGD Nov 2001)
db_adaptor = Bio::DB::GFF
db_args = -adaptor dbi::mysql
-dsn dbi:mysql:database=yeast;host=localhost
user = nobody
pass =
#this conf file is intended for use with the GFF3 file that SGD
#has made available. An out of date copy can be obtained from
#the gmod download page,
# http://prdownloads.sourceforge.net/gmod/saccharomyces_cerevisiae.gff.bz2?download
#or an up to date version can be obtained from
# ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/saccharomyces_cerevisiae.gff
#aggregators = transcript alignment orf
plugins = SequenceDumper FastaDumper RestrictionAnnotator
# where to link to when user clicks in detailed view
link = http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=$name
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
default features = Genes
tRNAs
# max and default segment sizes for detailed view
max segment = 500000
default segment = 50000
# examples to show in the introduction
examples = chrII
chrII:80,000..120,000
ChrMito
NPY1
NAB2
YGL123*
# "automatic" classes to try when an unqualified identifier is given
#automatic classes = Symbol Gene Clone
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
# a footer
footer = <hr>
<table width="100%">
<TR>
<TD align="LEFT" class="databody">
For the source code for this browser, see the <a href="http://www.gmod.org">
Generic Model Organism Database Project.</a> For other questions, send
mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
</TD>
</TR>
</table>
<hr>
<pre>$Id: 01.yeast.conf,v 1.6 2006-02-23 16:31:38 scottcain Exp $</pre>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
fontcolor = black
font2color = blue
label density = 25
bump density = 100
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[Centro:overview]
feature = centromere
bgcolor = blue
glyph = dot
fgcolor = black
height = 8
point = 1
key = Centromeres
[Genes]
feature = gene
glyph = generic
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height = 6
description = 1
key = Named gene
[CDS]
feature = CDS
glyph = cds
frame0f = cadetblue
frame1f = blue
frame2f = darkblue
frame0r = darkred
frame1r = red
frame2r = crimson
description = 0
height = 13
label = CDS 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
[Centro]
feature = centromere
glyph = span
bgcolor = blue
fgcolor = blue
height = 6
key = Centromeres
[Transp]
feature = transposable_element
glyph = segments
bgcolor = yellow
fgcolor = black
height = 5
stranded = 1
key = Transposons
[LTRs]
feature = repeat_region
fgcolor = black
glyph = anchored_arrow
height = 6
key = Repeats
[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)
[ncRNA]
feature = rRNA snRNA snoRNA
fgcolor = orange
glyph = generic
description = 1
key = Noncoding RNAs
[Landmark:overview]
feature = region:landmark
gbcolor = green
key = Landmarks
[Pseudogene]
feature = pseudogene
bgcolor = purple
key = Pseudogenes