[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  An out of date copy can be obtained from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
