# NOTE: This is the configuration file to start with when using Bio::DB::GFF databases
# created using the bioperl bp_genbank2gff.pl script
[GENERAL]
description = GenBank Tests
db_adaptor = Bio::DB::GFF
db_args = -adaptor dbi::mysql
-dsn dbi:mysql:database=genbank;host=localhost
-user nobody
-passwd ""
aggregators = mRNA{exon/mRNA} coding{CDS}
plugins = FastaDumper RestrictionAnnotator SequenceDumper
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
# 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 = ORIGIN GENE mRNA CDS tRNA repeat
# max and default segment sizes for detailed view
max segment = 1000000
default segment = 100000
# low-res boundary
low res = 200000
# zoom levels
zoom levels = 100 500 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
# canonical features to show in overview
overview units = M
overview bgcolor = wheat
detailed bgcolor = wheat
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: 08.genbank.conf,v 1.5 2005-12-09 22:19:09 mwz444 Exp $</pre>
# examples to show in the introduction
examples = CEF58D5 NC_001320 AP003256
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Sequence locus locus_tag gene standard_name protein_id
[TRACK DEFAULTS]
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
fontcolor = black
font2color = blue
label density = 25
bump density = 100
#######################################################################
# the remainder of the sections configure particular features to show
#######################################################################
[ORIGIN]
feature = region
glyph = anchored_arrow
fgcolor = orange
font2color = red
linewidth = 2
height = 10
description = 1
link = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=1&field=Sequence+ID&term=$name
key = Definition line
[GENE]
feature = gene
glyph = arrow
fgcolor = red
linewidth = 2
height = 6
description = 1
key = Annotated Genes
[mRNA]
feature = mRNA
glyph = transcript2
bgcolor = turquoise
fgcolor = black
height = 10
description = sub {
my $feature = shift;
my ($product) = $feature->attributes('product');
return $product;
}
key = Transcripts
[CDS]
feature = coding
glyph = transcript2
bgcolor = turquoise
fgcolor = black
height = 10
description = sub {
my $feature = shift;
return $feature->attributes('product');
}
key = Coding Regions
[tRNA]
feature = tRNA
bgcolor = white
fgcolor = black
curatedexon = slateblue
fontcolor = slateblue
height = 3
key = tRNAs
[repeat]
feature = repeat_region
glyph = segments
bgcolor = yellow
fgcolor = black
height = 5
stranded = 1
connector = dashed
key = Annotated Repeats
[DNA/GC Content]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
strand = both