# 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&amp;form=1&amp;field=Sequence+ID&amp;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
