# gbrowse config file for flybase D.pseudo # d.gilbert, jul04 [GENERAL] description = D. pseudoobscura Genome (R1.04) #datapath = /data/genomes/dpse/gnomap #datapath = /genomes/Drosophila_pseudoobscura/dpse_r10_20041216/gnomap datapath = /genomes/Drosophila_pseudoobscura/current/gnomap organism = D. pseudoobscura # synteny tests; 04oct synteny_idmap = dmel-synt-idmap.tsv synteny_org = D. melanogaster ##synteny_src = dmel synteny_src = dmel_r322 header =

FlyBase Genome Browser: D. pseudoobscura
Release 1.04, Dec 2004

NOTE: "Chromosome U" is an unordered collection of contigs that have not been located to a chromosome or ultracontig. These are artificially collected as "chromosome U" for display. Locations on U are not useful between contigs. footer =
Adapted from GBrowse of the Generic Model Organism Database Project. default_name = 2:100000-200000 default_range = 1-500000 # examples to show in the introduction # examples = # 2: 3: 2:3500000..3800000 # 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: # XL_group1a: XL_group1e: XL_group3b: XL_group3a: # XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: chromosomes = 2: 2_groupMISC: 3: 3_groupMISC: 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: 4_groupMISC: 5_groupMISC: XL_group1a: XL_group1e: XL_group3a: XL_group3b: XL_groupMISC: XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: XR_groupMISC: U: adaptor = flybase::gmod::FFFdb plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper default features = rev_ruler gene orthologous_region syntenic_region primary_feature = gene # scale_feature = cytoband # ignore these for now - NO? # feature_skip = cytoabs cytodef cytodup cytogene cytoins cytoinv cytotloc cytowalk dumpviews = FastA GenBank GFF FFF # dumpviews = dataviews = "Default" "Collapse All" "Expand All" # "Labelling On" uploads = 1 # 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 = 1000001 default segment = 100000 ## base range to expand around gene given ID lookup # expand_by = 60000 expand_by = 20000 zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 #searchhelp = #Search using Chromosome:base_start..end or FlyBase Gene ID. searchhelp = To find Dmel gene orthologs, use Find [Dmel\Gene_Symbol] with gene symbols prefixed by 'Dmel\', e.g. 'Dmel\Ubx', 'Dmel\cnn' searchitem = Find \n \n \n #panel property pad_left = 20 pad_right = 30 key_style = between key bgcolor = whitesmoke overview bgcolor = whitesmoke grid = 1 # put reversed features on same track or below ? mix_strand = 1 # # where to link to when user clicks in detaild view ## this dummy link allows title display; otherwise no url title :( # link = "#" # generic FB link - should work if FB id is in data link = sub { my $f= shift; my ($d); $d= $f->primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /^(GA|CG|CR|TE)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; } ($d)= $f->each_tag_value('note'); # best ids now 'hidden' in notes, Dbxref if ($d =~ /(FB\w\w\d+)/) { return '/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /((GA|CG|CR|TE)\d+)/ ){ return '/cgi-bin/fbidq.html?'.$1; } if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); } # or fbannq.html?name } ## NOTE: this is used by TextMapDumper plugin # my $link = $browser->config->code_setting($label,'dbx_link'); # $link = $browser->config->code_setting(general=>'dbx_link') unless defined $link; dbx_link = sub { my $dbx= shift; my $f= shift; #? my $r=''; foreach my $x (split(/[,;]\s*/,$dbx)) { my($h,$v); my($db,$ac)= split/:/,$x,2; if ($x =~ /(FB\w\w\d+)/) { $v=$1; $h= '/cgi-bin/fbidq.html?'.$v; } elsif ($db =~ /FlyBase/i) { $v=$ac; $h= '/cgi-bin/fbsymq.html?'.$ac; } elsif ($db eq 'GB_protein') { $v= $ac; $h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenBank&tool=FlyBase&term='.$ac; } elsif ($db eq 'GB') { $v= $ac; $h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$ac; } elsif ($db eq 'GO') { $v= $ac; $h= '/cgi-bin/goreport?id='.$ac; } if ($h && $v) { $r.= ''.$v.', '; } else { $r.= $x.', '; } } return $r; } # 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 # Default glyph settings glyph = generic height = 5 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 no_tick_label = 0 units = K link = key = Base ruler nodump = 1 keygroup = " Genomic features" [dna] feature = source glyph = dnabases draw_dna = 1 strand = forward label = 0 label density = 0 nodump = 1 key = DNA sequence keygroup = " Genomic features" link = [dnarev] feature = source glyph = dnabases draw_dna = 1 nodump = 1 strand = reverse label = 0 label density = 0 key = DNA reverse complement keygroup = " Genomic features" link = [gene] feature = gene mRNA glyph = transcript2 bgcolor = lightblue fgcolor = blue secondary = mRNA secondary_bgcolor = mediumblue secondary_fgcolor = mediumblue highlight_color = red higlighted = 1 label = 1 label density = 50 key = Gene Model keygroup = " Genomic features" citation = Gene and mRNA (transcript) features (annotation DB ; Chado) NOTNOW_link = sub { my $f= shift; my ($d); $d= $f->primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /^(GA)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; } elsif ($d =~ /^(C[GR]|TE)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; } ($d)= $f->each_tag_value('note'); # best ids now 'hidden' in notes, Dbxref if ($d =~ /(FB\w\w\d+)/) { return '/cgi-bin/fbidq.html?'.$1; } if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); } # or fbannq.html?name } NOTrename = sub { my $f= shift; my $tn= $f->info; my ($nt)= $f->each_tag_value('note'); if ($nt =~ m/ortholog\w+=FlyBase:([^;,]+)/) { $tn .= " Dmel\\".$1; } return $tn; } title = sub { my $f= shift; my $t= $f->class .":". $f->info; my ($nt)= $f->each_tag_value('note'); if ($nt =~ m/ortholog\w+=FlyBase:([^;,]+)/) { $t .= " Dmel\\".$1; } $t .= " ". $f->seq_id .':'.$f->start."..".$f->end; return $t; } [CDS] feature = CDS # glyph = translation glyph = segments stranded = 1 translation = 1frame bgcolor = palegoldenrod fgcolor = goldenrod label = 1 key = CDS citation = Protein coding sequence (CDS or translation; annotation DB ; Chado) keygroup = " Genomic features" #link = "#" # [orthogene] # feature = gene orthologous_region # glyph = transcript2 # fgcolor = blue # bgcolor = palegoldenrod # secondary = gene # secondary_bgcolor = palegoldenrod # secondary_fgcolor = brown # label = 1 # label density = 50 # height = 4 # key = Orthogene # citation = Orthologous_region # keygroup = " Synteny features" # ## if use rename() need to use $f->id()? for link # link = sub { my $f= shift; my $tp= $f->primary_tag; # my ($id)= $f->each_tag_value('id'); # if ($tp eq 'gene') { return '/cgi-bin/fbidq.html?'.$id; } # #my ($id)= $f->each_tag_value('id'); # unless ($id) { my $nm= $f->name(); $id= $nm if ($nm=~/^ortho:/); } # if ($id) { return '?syn='.$id; } # } # rename = sub { my $f= shift; my $tn= ''; # my ($nt)= $f->each_tag_value('note'); # if ($nt =~ m/to_species=([^;,]+)/) { $tn .= ucfirst($1).'\\'; } # if ($nt =~ m/to_name=([^;,]+)/) { $tn .= $1; } # $tn ||= $f->info; # return $tn; # } [orthologous_region] feature = orthologous_region glyph = transcript2 # glyph = segments # no_arrows = 0 bgcolor = palegoldenrod fgcolor = turquoise label = 1 label density = 50 height = 4 key = Ortholog citation = Orthologous_region keygroup = " Synteny features" link = sub { my $f= shift; my ($nt)= $f->each_tag_value('note'); #to_name=CG31119-PA;to_species=dmel if ($nt =~ m/to_name=[^; ]*((CG|CR|TE)\d+)/) { return '/cgi-bin/fbidq.html?'.$1; } my ($id)= $f->each_tag_value('id'); unless ($id) { my $nm= $f->name(); $id= $nm if ($nm=~/^ortho:/); } if ($id) { return '?syn='.$id; } } rename = sub { my $f= shift; my $tn= ''; my ($nt)= $f->each_tag_value('note'); if ($nt =~ m/to_name/){ if ($nt =~ m/to_species=([^;,]+)/) { $tn .= ucfirst($1).'\\'; } if ($nt =~ m/to_name=([^;,]+)/) { my $n=$1; $n=~s/-\w\w//; $tn .= $n; } } $tn ||= $f->info; # == ortho:nnn, not wanted return $tn; } title = sub { my $f= shift; my $t= $f->class .":". $f->info; my ($nt)= $f->each_tag_value('note'); if ($nt =~ m/to_name=[^; ]*((CG|CR|TE)\d+)/) { my $oid=$1; $t .= " ".$oid unless($t=~/$oid/); } $t .= " ". $f->seq_id .':'.$f->start."..".$f->end; return $t; } # title = sub { my $f= shift; my $tn= ''; my $nt; # $nt= $f->each_tag_value('note'); ##$nt ||= $f->description; # if ($nt =~ m/to_species=([^;,]+)/) { $tn .= $1.'\\'; } # if ($nt =~ m/to_name=([^;,]+)/) { $tn .= $1; } # $tn ||= $f->info; # return $f->class .":". $tn . " ". $f->seq_id .':'.$f->start."..".$f->end; # } [syntenic_region] feature = syntenic_region glyph = segments #glyph = transcript2 bgcolor = pink fgcolor = darkred label = 1 key = Syntenic region citation = Syntenic_region keygroup = " Synteny features" link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } } [gene_genscan] feature = gene:genscan mRNA:genscan glyph = transcript2 bgcolor = tan fgcolor = brown secondary = mRNA:genscan secondary_bgcolor = lightslategray label = 1 key = Gene (Genscan) citation = Genscan predicted Gene and mRNA keygroup = "Analysis features" link = "#" [gene_genewise] feature = gene:genewise mRNA:genewise glyph = transcript2 bgcolor = lightgreen fgcolor = green secondary = mRNA:genewise secondary_bgcolor = lightslategray label = 1 key = Gene (Genewise) citation = Genewise predicted Gene and mRNA keygroup = "Analysis features" link = "#" [gene_twinscan] feature = gene:twinscan mRNA:twinscan glyph = transcript2 bgcolor = yellow fgcolor = orange secondary = mRNA:twinscan secondary_bgcolor = lightslategray label = 1 key = Gene (Twinscan) keygroup = "Analysis features" citation = Twinscan predicted Gene and mRNA link = "#" [mb_nadbESTdpse] feature = match:blastn:na_dbEST.dpse glyph = segments stranded = 1 bgcolor = lightslategray fgcolor = black key = Dpse dbEST citation = match:blastn:na_dbEST.dpse keygroup = "Analysis features" link = sub { my $v=shift->name(); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } [m_blastz] feature = match:blastz glyph = segments stranded = 1 bgcolor = lightslategray fgcolor = black key = match:blastz citation = match:blastz keygroup = "Analysis features" link = "#" NOTlink = sub { my $v=shift->name(); $v=~s/^(GB)[:]//; $v=~s/[:.].*$//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } [mt_Dmelr31] feature = match:tblastn:Dmel_r3.1 glyph = segments stranded = 1 bgcolor = lightslategray fgcolor = black key = Dmel r31 transcript citation = match:tblastn:Dmel_r3.1 keygroup = "Analysis features" link = sub { my $v=shift->name(); $v=~s/^(GB)[:]//; $v=~s/[:.].*$//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } [blast] feature = blast glyph = alignment bgcolor = darkorchid fgcolor = darkorchid bump = 1 label = 1 key = Blast hit height = 8 citation = BLAST alignment hit keygroup = "hidden" link = "#" # [contig] # feature = contig # glyph = extending_arrow # no_arrows = 1 # #west = 1 # base = 0 # bgcolor = lightslategray # fgcolor = lightslategray # linewidth = 2 # bump = 1 # label = 1 # key = Contig # citation = Contig (annotation DB ; Chado) # keygroup = " Genome reagents" # # link = sub { my $f= shift; # # return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; } ## bad data in dpse chado db #[NOTscaffold] #feature = NOTscaffold #glyph = anchored_arrow #no_arrows = 1 #base = 0 #fgcolor = black #bgcolor = black #linewidth = 2 #bump = 1 #label = 1 #height = 4 #key = GenBank Scaffold #citation = segment (annotation DB ; Chado) #keygroup = " Genome reagents" #link = sub { my $nm= shift->name(); return ($nm)?'/cgi-bin/fbannq.html?ARM='.$nm : ''; }