[GENERAL] description = Volvox Example Database db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor memory -dir '/usr/local/apache/doc/gbrowse/databases/volvox' plugins = drag and drop = 1 balloon tips = 1 titles are balloons = 1 # list of tracks to turn on by default default features = ExampleFeatures # examples to show in the introduction examples = ctgA # what image widths to offer image widths = 450 640 800 1024 # default width of detailed view (pixels) default width = 800 # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons tmpimages = /gbrowse/tmp # feature to show on startup initial landmark = ctgA:1..10000 # max and default segment sizes for detailed view max segment = 50000 default segment = 5000 # zoom levels zoom levels = 100 200 1000 2000 5000 10000 20000 40000 50000 # colors of the overview, detailed map and key overview bgcolor = lightgrey detailed bgcolor = lightgoldenrodyellow key bgcolor = beige label density = 25 bump density = 100 # "automatic" classes to try when an unqualified identifier is given automatic classes = Gene Protein # other customization options... # HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS # inside the section head = # at the top... header = # a footer footer =
$Id: volvox4.conf,v 1.5.8.1.2.1 2009/08/05 13:24:11 scottcain Exp $
# Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic' ######################## # Default glyph settings ######################## [TRACK DEFAULTS] glyph = generic height = 10 bgcolor = lightgrey fgcolor = black font2color = blue label density = 25 bump density = 100 # where to link to when user clicks in detailed view link = AUTO ################## TRACK CONFIGURATION #################### # the remainder of the sections configure individual tracks ########################################################### [ExampleFeatures] feature = remark glyph = generic stranded = 1 bgcolor = blue height = 10 key = Example Features [Motifs] feature = polypeptide_domain glyph = span height = 5 description = 1 key = Example motifs [Alignments] feature = match glyph = segments key = Example alignments [Genes] feature = gene glyph = gene bgcolor = peachpuff label_transcripts = 1 draw_translation = 1 category = Genes key = Protein-coding genes [Transcripts] feature = processed_transcript gene glyph = processed_transcript height = 8 bgcolor = black utr_color = black thin_utr = 1 decorate_introns = 1 description = 1 key = Protein-coding genes [CDS] feature = CDS:predicted glyph = gene bgcolor = white category = Genes key = Predicted genes [Transcript] feature = mRNA:exonerate glyph = so_transcript description = 1 bgcolor = beige category = Genes key = Exonerate predictions [ReadingFrame] feature = mRNA glyph = cds ignore_empty_phase = 1 category = Genes key = Frame usage [Clones] feature = BAC glyph = segments bgcolor = yellow connector = dashed strand_arrow = 1 description = 1 key = Fingerprinted BACs [TransChip] feature = microarray_oligo glyph = wiggle_density height = 30 bgcolor = blue category = Genes description = 1 key = Transcriptional Profile [DNA] glyph = dna global feature = 1 height = 40 do_gc = 1 gc_window = auto fgcolor = red axis_color = blue strand = both key = DNA/GC Content [Translation] glyph = translation global feature = 1 height = 40 fgcolor = purple start_codons = 0 stop_codons = 1 translation = 6frame key = 6-frame translation [EST] feature = EST_match:est glyph = segments height = 6 draw_target = 1 show_mismatch = 1 canonical_strand = 1 bgcolor = sub { my $feature = shift; my $name = $feature->display_name; if ($name =~ /\.5$/) { return 'red'; } else { return 'orange'; } } group_pattern = /\.[53]$/ key = ESTs