Briggsae.synconf
From GMOD
This is the species database for C. briggsae. This is one of the three species currently represented in the instance of Gbrowse_Syn that is installed at WormBase. The species config file con be a normal Gbrowse config file or can a a simplified version as shown here.
[GENERAL]
description = C. briggsae (current release)
adaptor = dbi::mysqlopt
database = dbi:mysql:database=briggsae;host=localhost
user = nobody
aggregators = wormbase_cds{coding_exon/CDS}
tmpimages = sub {
my ($server) = $ENV{SERVER_NAME} =~ /(.*?)\..*/;
$server ||= 'local';
return
"/ace_images/gbrowse/$server","/var/tmp/ace_images/gbrowse";
}
##################################################################################
# the remainder of the sections configure particular tracks to show
##################################################################################
[WBG]
feature = wormbase_cds:curated wormbase_cds:history
glyph = wormbase_transcript
reversecolor = sub { pop->panel->flip ? 'violet' : 'turquoise' }
forwardcolor = sub { pop->panel->flip ? 'turquoise' : 'violet' }
key = Curated ("hybrid") genes
fgcolor = black
font2color = blue
height = 10
description = sub { my @notes = shift->notes; join '; ',@notes }
link = /db/gene/gene?name=$name
title = curated gene $name
category = Genes
citation = These are "best" gene predictions that have been selected from the raw
gene set on several criteria: (1) whether the gene has a mutual-best-hit
ortholog in C. elegans; (2) whether the gene has a high-similarity hit in
C. elegans; (3) whether multiple gene prediction programs produce the same
or similar structure. The detailed method is described in
<a href="http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000045">
Stein et al., 2003</a>
