# gbrowse config file for flybase overview gene maps # d.gilbert, aug02 # set for use in flybase portable server (all paths and urls are relative) ## WARNING - gbrowse plumbing is now doing lc(key) on all config keys ! [GENERAL] description = D. melanogaster Overview (R3.2.2) #datapath = /data2/fban/gnomap datapath = /genomes/Drosophila_melanogaster/dmel_r3.2.2_10212004/gnomap #datapath = /data2/fban/current/gnomap organism = D. melanogaster # synteny tests; 04oct synteny_idmap = dpse-synt-idmap.tsv synteny_org = D. pseudoobscura synteny_src = dpse_overview #header =

FlyBase Genome Browser

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FlyBase Genome Overview: D. melanogaster
Release 3.2.2; Oct 2004

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Adapted from GBrowse of Generic Model Organism Database Project. ## expects adaptor to be subclass of Bio/DB/GFF/Adaptor/ adaptor = flybase::gmod::FFFdb default_name = X: default_range = 1-30000000 # examples to show in the introduction chromosomes = X: 2L: 2R: 3L: 3R: 4: default features = cytosegment syntenic_region scaffold BAC primary_feature = scaffold scale_feature = cytoband # scaffold was segment .. so term change plugins = # plugins = BatchDumper TextMapDumper FastaDumper GFFDumper uploads = 0 dumpviews = # FastA GenBank GFF FFF dataviews = # "Default" "Collapse All" "Expand All" "Gene Labelling On" # Web site configuration info # stylesheet = /templates/gbrowse.css # help = /maps/gbrowse help = /common/perl/gbrowse_fb/htdocs stylesheet = /common/perl/gbrowse_fb/gbrowse.css buttons = /common/perl/gbrowse_fb/images/buttons tmpimages = /tmp/gbrowse_fb #bac_insitu_pic = /images/lk/bac_insitu_pic # max num bac image display (set to 0 to disable) #max bac pic = 0 # max and default segment sizes for detailed view max segment = 100000000 default segment = 20000000 ## base range to expand around gene given ID lookup # expand_by = 60000 expand_by = 20000 zoom levels = 500000 1000000 5000000 10000000 20000000 30000000 searchhelp = # Search using Chromosome:base_start..end or FlyBase Gene ID. #panel property pad_left = 20 pad_right = 30 pad_top = 10 pad_bottom = 10 key_style = between key bgcolor = whitesmoke overview bgcolor = whitesmoke grid = 0 # put reversed features on same track or below ? mix_strand = 1 ## where to link to when user clicks in detaild view -- go to detailed gbrowse ## NOTE need proper config source name here link = sub { my $f=shift; my $u=$ENV{REQUEST_URI}; my $r= $f->ref.":".$f->to_FTstring.";doexpand=1"; $u =~ s/\?.*$//; $u .= '?source=dmel&name='.$r; return $u; } # title = sub { my $f=shift; return ($f->name())? $f->name(): "" ; } # make_title in Browser should be doing this, but get only "Gene" == class? ## the perl syntax ->method||'' was causing failure ! title = sub { my $f= shift; return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end; } # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone # Default glyph settings glyph = generic height = 8 bgcolor = palegoldenrod fgcolor = cyan boxcolor = blue label density = 20 bump density = 50 overview label density = 160 image widths = 450 640 800 950 1024 # default width of detailed view (pixels) default width = 800 width = 800 #---------- end [GENERAL] ------------------------ ##? these sections seem to work only per GMOD->track not per feature ?? # bperl equates [label] with feature type # [rev_ruler] # glyph = ruler_arrow # label = 0 # no_53_label = 1 # label_align = center # tick = 1 # #both = 1 # no_tick_label = 0 # units = M # key = Base ruler # keygroup = " Genomic features" # #height = 0 # #linewidth = 0 [cytosegment] feature = cytoband_major glyph = generic # glyph = anchored_arrow fgcolor = black bgcolor = lightgreen # height = 5 linewidth = 1 label = 1 label density = 10000 bump = 0 bump density = 0 label_align = center key = Cytology segment keygroup = " Genomic features" # link = sub { my $f=shift; my $u=$ENV{REQUEST_URI}; # my $r= $f->ref.":".$f->to_FTstring.";doexpand=1"; # $u =~ s/\?.*$//; $u .= '?name='.$r; # # $u =~ s/\;doexpand=\d+//g; $u =~ s/(\W)(id|name)[^\;\,\+\&]*/${1}name=$r/i; # return $u; # } # feature = cytoband_major cytoband # secondary = cytoband # secondary_bgcolor = green # secondary_fgcolor = green [gene] feature = gene glyph = transcript2 bgcolor = mediumblue fgcolor = blue # secondary = mRNA # secondary_bgcolor = mediumblue # secondary_fgcolor = mediumblue # highlight_color = red # higlighted = 1 label = 1 label density = 50 # height = 6 key = Gene link = sub { my $f= shift; my $u='/.bin/'; my $d= $f->primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d =~ /(FB\w\w\d+)/){ $u .= 'fbidq.html?'.$1; } else { $u.='fbgenq.html?symbol='.$f->name(); } return $u ; } keygroup = " Genomic features" # [pseudogene] # feature = pseudogene # glyph = segments # #glyph = anchored_arrow # fgcolor = orange # # height = 6 # label = 1 # key = Pseudogene [RNA] feature = tRNA ncRNA snoRNA snRNA miscRNA glyph = generic bgcolor = peachpuff height = 4 stranded = 1 key = Non-coding RNAs keygroup = " Genomic features" [syntenic_region] feature = syntenic_region glyph = segments bgcolor = pink fgcolor = darkred label = 1 bump = 1 bump density = 1000 key = Syntenic region citation = Syntenic_region keygroup = " Genomic features" # link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } } # [transposable_element] # feature = transposable_element # # fgcolor = violet # bgcolor = magenta # fgcolor = magenta # label = 1 # glyph = anchored_arrow # # height = 5 # key = Transposon # [EST] # feature = cDNA_clone EST # glyph = segments # bgcolor = lightgreen # fgcolor = green # secondary = cDNA_clone # secondary_bgcolor = mediumseagreen # secondary_fgcolor = mediumseagreen # # bump = 1 # key = cDNA and EST # link = http://www.fruitfly.org/cgi-bin/EST/community_query/ctgReport.pl?db=estlabtrack&id_type=0&id_value=$info # #max_score = 100 # [repeat_region] # feature = repeat_region # glyph = segments # bgcolor = darkorchid # fgcolor = darkorchid # height = 4 # connector = solid # bump = 1 # label = 0 # key = Repeat region # keygroup = " Genomic features" [BAC] feature = BAC glyph = generic #glyph = extending_arrow no_arrows = 1 base = 0 bgcolor = #DD66DD fgcolor = black linewidth = 1 bump = 1 bump density = 1000 label = 1 key = Tiling BAC keygroup = " Genomic features" # link = sub { my $f= shift; # return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; } [scaffold] feature = golden_path scaffold glyph = generic # glyph = anchored_arrow # anchored_arrow no_arrows = 1 #northeast = 1 base = 0 fgcolor = black bgcolor = yellow linewidth = 1 bump = 1 bump density = 1000 label = 1 key = GenBank Scaffold keygroup = " Genomic features" # relative_coords = 1 # link = sub { my $f= shift; # return ($f->name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; } ### cytos [cytobreakpoint_other] feature = cytobreakpoint_other glyph = cytobar bgcolor = lightslategray fgcolor = lightslategray connector = dashed connector_color = #8888FF bump = 1 label = 1 key = Other breakpoints (cytol.) citation = Other breakpoints (cytology mapped) height = 4 keygroup = "Cytology mapped features" [cytodeleted_segment] feature = cytodeleted_segment glyph = cytobar bgcolor = lightslategray fgcolor = lightslategray connector = dashed connector_color = #ff00aa bump = 1 label = 1 key = Deleted segments (cytol.) citation = Deleted segments (cytology mapped) height = 2 keygroup = "Cytology mapped features" [cytoduplicated_segment] feature = cytoduplicated_segment glyph = cytobar bgcolor = lightslategray fgcolor = lightslategray connector = dashed connector_color = #88FF88 bump = 1 label = 1 key = Duplicated segments (cytol.) citation = Duplicated segments (cytology mapped) height = 2 keygroup = "Cytology mapped features" [cytobreakpoint_inv] feature = cytobreakpoint_inv glyph = cytobar bgcolor = lightslategray fgcolor = lightslategray connector = dashed connector_color = #FF9900 bump = 1 label = 1 key = Inversion breakpoints (cytol.) citation = Inversion breakpoints (cytology mapped) height = 4 keygroup = "Cytology mapped features" [cytobreakpoint_ttp] feature = cytobreakpoint_ttp glyph = cytobar bgcolor = lightslategray fgcolor = lightslategray connector = dashed bump = 1 label = 1 key = Translocations & Transpositions (cytol.) citation = Translocation & Transposition breakpoints (cytology mapped) height = 4 keygroup = "Cytology mapped features" [cytoins] feature = cytoins glyph = cytobar connector_color = #ffbb00 bgcolor = lightslategray fgcolor = lightslategray connector = dashed bump = 1 label = 1 key = Transgene insertion (cytol.) citation = Chromosomal Insertion (cytologically mapped; CytoSearch DB) height = 2 keygroup = "Cytology mapped features" [cytogene] feature = cytogene glyph = cytobar connector = dashed connector_color = #ffaa00 bgcolor = lightslategray fgcolor = lightslategray connector = dashed bump = 1 label = 1 key = Gene (recomb. only) citation = Genes mapped by cytology/recombination data only (possible orphans; cytologically mapped; CytoSearch DB) height = 4 keygroup = "Cytology mapped features"