From: Nalini K. C. <nal...@gm...> - 2015-11-06 21:38:22
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[GENERAL] description = Arabidopsis Database database = arab initial landmark = NC_003070 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1 default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region # examples to show in the introduction examples = NC_003070 NC_003071 NC_003074 NC_003075 NC_003076 # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ################################# # database definitions ################################# [scaffolds:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor dbi::mysql -dir /var/lib/gbrowse2/databases/Arabidopsis -dsn dbi:mysql:databases=arab;host=localhost -gff '/var/lib/gbrowse2/databases/Arabidopsis' search options = default +autocomplete user = apache pass = # Default glyph settings [TRACK DEFAULTS] glyph = generic database = annotations height = 8 bgcolor = cyan fgcolor = black label density = 25 bump density = 100 show summary = 99999 # go into summary mode when zoomed out to 100k ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [Centro:overview] feature = centromere bgcolor = blue glyph = dot fgcolor = black height = 8 point = 1 show summary = 0 # no summary of this one key = Centromeres [tRNA:overview] feature = tRNA glyph = generic bgcolor = lightgray fgcolor = black height = 4 stranded = 1 description = 1 show summary = 0 # no summary of this one key = tRNAs [GC:region] glyph = dna global feature = 1 database = scaffolds height = 40 gc_window = auto do_gc = 1 strand = both fgcolor = red axis_color = blue show summary = 0 # no summary of this one key = GC Content [Genes] feature = gene glyph = gene bgcolor = yellow forwardcolor = yellow reversecolor = turquoise label = sub { my $f = shift; my $name = $f->display_name; my @aliases = sort $f->attributes('Alias'); $name .= " (@aliases)" if @aliases; $name; } height = 6 description = 0 key = Named gene [CDS] feature = gene glyph = cds description = 0 height = 26 sixframe = 1 label = sub {shift->name . " reading 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 [Transp] feature = LTR_retrotransposon glyph = segments bgcolor = yellow fgcolor = black height = 5 stranded = 1 key = Transposons [LTRs] feature = long_terminal_repeat fgcolor = black glyph = anchored_arrow height = 6 key = Long Terminal Repeats [Translation] glyph = translation global feature = 1 database = scaffolds height = 40 fgcolor = purple strand = +1 translation = 6frame key = 6-frame translation [TranslationF] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = purple strand = +1 translation = 3frame key = 3-frame translation (forward) [DNA/GC Content] glyph = dna global feature = 1 database = scaffolds height = 40 do_gc = 1 gc_window = auto strand = both fgcolor = red axis_color = blue [TranslationR] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = blue strand = -1 translation = 3frame key = 3-frame translation (reverse) [ncRNA] feature = RNAd rRNA:sgd snRNA:sgd snoRNA:sgd fgcolor = orange glyph = generic description = 1 key = Noncoding RNAs |