# 07.dmel41my.conf # gbrowse config file for gff mysql-indexed gene features # d.gilbert, may05 #slight modifications by Scott Cain to include with GBrowse dist # should work well with current flybase GFF3 [GENERAL] description = D. melanogaster (dmelr41; MySQL) header =

D. melanogaster Genome, Annotation Release 4.1; Feb 2005 using MySQL-GFF data adaptor

adaptor = dbi::mysql database = dbi:mysql:database=flybase user = nobody passwd = aggregators = transcript alignment default name = 4:100000-200000 # examples to show in the introduction examples = X 2L 2R 3L 3R 4 chromosome_arm:4 2L:80,000..120,000 4:200000..500000 plex* Ank Gadfly:CG11186 FlyBase:FBan0011186 plugins = BatchDumper FastaDumper GFFDumper cache_overview = 360 cachedir = 360 # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons tmpimages = /gbrowse/tmp help = /gbrowse/ # Default glyph settings glyph = generic height = 8 bgcolor = cyan fgcolor = cyan label density = 25 bump density = 100 # where to link to when user clicks in detaild view # NOTlink =AUTO # generic FB link - should work if FB id is in data link = sub { my $f= shift; my $d= join(',',$f->each_tag_value('ID'),$f->id(),$f->each_tag_value('Dbxref')); my $tp= $f->class; my $best='(FB\w\w\d+)'; if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan? elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; } elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; } elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; } elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; } if ($d =~ /$best/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /(FB\w\w\d+)/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; } if ($f->name()) { return 'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); } } title = sub { my $f= shift; return $f->method .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end; } ## suggested display name change ? is this active ## this works .. but cant do at general level here; needs to be in each feature def label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } # what image widths to offer image widths = 450 640 800 1024 # default width of detailed view (pixels) default width = 800 default features = gene scaffold # max and default segment sizes for detailed view max segment = 1000001 default segment = 100000 # low-res boundary low res = 200000 # zoom levels zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 # colors of the overview, detailed map and key overview units = M overview bgcolor = lightgrey detailed bgcolor = lightgoldenrodyellow key bgcolor = beige # "automatic" classes to try when an unqualified identifier is given automatic classes = Gene Symbol language = en # a footer footer =
For the source code for this browser, see the Generic Model Organism Database Project. For other questions, send mail to lstein@cshl.org. 
$Id: 03.fly.conf,v 1.2.6.2 2005/10/10 13:41:06 scottcain Exp $
# Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [gene] feature = gene transcript glyph = transcript2 bgcolor = lightblue fgcolor = blue secondary = mRNA secondary_bgcolor = mediumblue secondary_fgcolor = mediumblue highlight_color = red higlighted = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } label density = 50 bump density = 150 key = Gene Model category = ' Genomic features' citation = Gene and mRNA (transcript) features (annotation DB ; Chado) [genespan] feature = gene glyph = segments stranded = 1 bgcolor = lightblue fgcolor = blue highlight_color = red higlighted = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } label density = 50 bump density = 150 key = Gene span category = ' Gene Model subfeatures' citation = Gene span features (annotation DB ; Chado) # an aggregator feature [mRNA] feature = transcript glyph = segments stranded = 1 translation = 1frame bgcolor = palegoldenrod fgcolor = goldenrod label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = mRNA citation = Transcript (mRNA; annotation DB ; Chado) category = ' Gene Model subfeatures' [CDS] feature = CDS glyph = segments stranded = 1 translation = 1frame bgcolor = palegoldenrod fgcolor = goldenrod #label = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = CDS citation = Protein coding sequence (CDS or translation; annotation DB ; Chado) category = ' Gene Model subfeatures' [intron] feature = intron glyph = segments stranded = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = intron citation = intron category = ' Gene Model subfeatures' link = "#" [five_prime_UTR] feature = five_prime_UTR glyph = segments stranded = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = 5prime UTR citation = five_prime_UTR category = ' Gene Model subfeatures' link = "#" [three_prime_UTR] feature = three_prime_UTR glyph = segments stranded = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = 3prime UTR citation = three_prime_UTR category = ' Gene Model subfeatures' link = "#" #--------------------------------- [pseudogene] feature = pseudogene glyph = segments strand_arrow = 1 fgcolor = orange label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = Pseudogene category = ' Genomic features' [tRNA] feature = tRNA bgcolor = white fgcolor = black curatedexon = slateblue fontcolor = slateblue height = 3 key = tRNAs category = ' Genomic features' [noncodingRNA] feature = ncRNA snoRNA snRNA miscRNA glyph = generic bgcolor = peachpuff height = 4 stranded = 1 key = Various non coding RNAs category = ' Genomic features' [transposable] feature = transposable_element bgcolor = magenta fgcolor = magenta label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } glyph = anchored_arrow key = Natural transposon citation = Natural transposon (annotation DB ; Chado) category = ' Genomic features' [tinsert] feature = transposable_element_insertion_site glyph = pinsertion bgcolor = darkturquoise fgcolor = darkturquoise bump = 1 label = 0 key = Transgene insertion site citation = Transgene insertion site (annotation DB ; Chado) category = ' Genomic features' link = sub { my $f= shift; my($d); $d= join(',',$f->each_tag_value('ID'),$f->each_tag_value('Dbxref'),$f->primary_id()); if ($d =~ /(FBti\d+)/||$d =~ /((FB\w\w|TE)\d+)/) { return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; } if ($f->name()) { return 'http://flybase.org/cgi-bin/fbinsq.html?symbol='.$f->name(); } } #-------- Misc. Genomic features ------------------- [polyA_site] feature = polyA_site #glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = polyA_site citation = polyA_site (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } # Gsc-polyA_site-585205..585205 2L [point_mutation] feature = point_mutation # glyph = segments bgcolor = lightslategray fgcolor = lightslategray key = point_mutation citation = point_mutation (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [protein_binding_site] feature = protein_binding_site # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = protein_binding_site citation = protein_binding_site (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [rescue_fragment] feature = rescue_fragment # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = rescue_fragment citation = rescue_fragment (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [mature_peptide] feature = mature_peptide glyph = segments strand_arrow = 1 bgcolor = palegoldenrod fgcolor = orange key = mature_peptide citation = mature_peptide (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [enhancer] feature = enhancer # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = enhancer citation = enhancer (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [aberration_junction] feature = aberration_junction # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = aberration_junction citation = aberration_junction (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } # add: regulatory_region and sequence_variant [regulatory_region] feature = regulatory_region # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = regulatory_region citation = regulatory_region (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [sequence_variant] feature = sequence_variant # glyph = segments strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = sequence_variant citation = sequence_variant (annotation DB ; Chado) category = ' Misc. Genomic features' link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v; } [DNA_motif] feature = DNA_motif RNA_motif # glyph = segments bgcolor = plum fgcolor = plum secondary = RNA_motif secondary_bgcolor = mediumseagreen secondary_fgcolor = mediumseagreen strand_arrow = 1 bump = 1 label = 0 key = DNA / RNA motif citation = DNA_motif and RNA_motif (annotation DB ; Chado) category = ' Misc. Genomic features' link = "#" [chromosome_band] feature = chromosome_band glyph = generic bgcolor = blue fgcolor = blue height = 4 key = chromosome_band ##category = ' Misc. Genomic features' #---------- Small Genome reagents -------------- [DGC] feature = match:sim4:na_DGC_dros glyph = segments strand_arrow = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } bgcolor = plum fgcolor = black key = DGC EST/cDNA citation = DGC cDNA_clone (annotation DB ; Chado) category = ' Genome reagents' link = sub { my $f= shift; my $v= $f->name(); my @v= $f->each_tag_value('Name'); $v= shift @v if (@v>0); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } [EST] feature = match:sim4:na_dbEST.same.dmel match:sim4:na_dbEST.diff.dmel glyph = segments strand_arrow = 1 bgcolor = lightgreen fgcolor = green key = EST citation = EST (annotation DB ; Chado) category = ' Genome reagents' 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; } #drop from link name: .5prime_revcomp .5prime, :contig1, SD02026:contig1, CK02552.5prime # but for ones like GB:AV399447 drop db: [oligo] feature = oligo glyph = generic bgcolor = tomato fgcolor = tomato height = 4 bump = 0 bump density = 1 label = 0 label density = 0 key = Affy Oligo citation = oligonucleotide (annotation DB ; Chado) category = ' Genome reagents' link = sub { my $f= shift; return ($f->name())?'http://flybase.org/cgi-bin/fbannq.html?oligo='.$f->name() : ''; } #-------- Analysis ------------------- # from match:promoter ? [transcription_start_site] feature = transcription_start_site glyph = generic bgcolor = purple fgcolor = purple bump = 1 label = 0 label density = 0 key = Promoter prediction citation = Transcription promoter prediction (annotation DB ; Chado) category = ' Analysis features' link = "#" [repeat_region] feature = repeat_region match:repeat_runner_seg match:repeatmasker # glyph = extending_arrow bgcolor = darkorchid fgcolor = darkorchid height = 3 connector = solid bump = 1 strand_arrow = 0 label = 0 label density = 0 key = Repeat region citation = repeat_region (annotation DB ; Chado) category = ' Analysis features' link = "#" [mRNA_genscan] feature = mRNA_genscan match:genscan glyph = segments strand_arrow = 1 bgcolor = tan fgcolor = brown connector = solid bump = 1 label = sub { my $f = shift; my @n = ($f->attributes('Name'), $f->attributes('Alias')); return $n[0] || $f->display_name; } key = Genscan prediction citation = Genscan (gene prediction) (annotation DB ; Chado) category = ' Analysis features' link = "#" [mRNA_genie] feature = mRNA_piecegenie match:genie glyph = segments strand_arrow = 1 bgcolor = yellow fgcolor = brown connector = solid bump = 1 label = 0 label density = 0 key = Genie prediction citation = PieceGenie (gene prediction) (annotation DB ; Chado) category = ' Analysis features' link = "#" [match_HDP] feature = match:HDP glyph = segments strand_arrow = 1 bgcolor = yellow fgcolor = brown connector = solid bump = 1 label = 0 key =HDP prediction citation = HDP (annotation DB ; Chado) category = ' Analysis features' link = "#" [match_RNAiHDP] feature = match:RNAiHDP glyph = segments strand_arrow = 1 bgcolor = tan fgcolor = brown connector = solid bump = 1 label = 0 key = RNAiHDP prediction citation = RNAiHDP (annotation DB ; Chado) category = ' Analysis features' link = "#" [tRNA_trnascan] feature = tRNA:trnascan glyph = transcript2 bgcolor = yellow fgcolor = brown connector = solid bump = 1 label = 0 key = tRNAscan prediction citation = tRNAscan (tRNA prediction) (annotation DB ; Chado) category = ' Analysis features' link = "#" #-- BLAST features; combined some [mb_aa_SPTR.dmel] feature = match:blastx:aa_SPTR.dmel glyph = segments bgcolor = lightslategray fgcolor = black key = D melanogaster protein citation = match:blastx:aa_SPTR.dmel category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mx_nadpse] feature = match:tblastx:na_dpse glyph = segments bgcolor = lightslategray fgcolor = black label = 1 link = AUTO #sub {my $v=shift->name(); $v=~s/\-\d+.*$//; return '?source=dpse_overview&id='.$v if($v); } key = D pseudoobscura contigs citation = match:tblastx:na_dpse category = ' Blast features' [mb_na_agambiae] feature = match:tblastx:na_agambiae glyph = segments bgcolor = lightslategray fgcolor = black key = Mosquito NA citation = match:tblastx:na_agambiae category = ' Blast 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; } [mb_aa_SPTR.insect] feature = match:blastx:aa_SPTR.insect glyph = segments bgcolor = lightslategray fgcolor = black key = Insect protein citation = match:blastx:aa_SPTR.insect category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_na_dbEST.insect] feature = match:tblastx:na_dbEST.insect glyph = segments bgcolor = lightslategray fgcolor = black key = Insect dbEST citation = match:tblastx:na_dbEST.insect category = ' Blast 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; } [mb_aa_SPTR.worm] feature = match:blastx:aa_SPTR.worm glyph = segments bgcolor = lightslategray fgcolor = black key = Worm protein citation = match:blastx:aa_SPTR.worm category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_aa_SPTR.yeast] feature = match:blastx:aa_SPTR.yeast glyph = segments bgcolor = lightslategray fgcolor = black key = Yeast protein citation = match:blastx:aa_SPTR.yeast category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_aa_SPTR.othinv] feature = match:blastx:aa_SPTR.othinv glyph = segments bgcolor = lightslategray fgcolor = black key = Other invert. protein citation = match:blastx:aa_SPTR.othinv category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_aa_SPTR.primate] feature = match:blastx:aa_SPTR.primate glyph = segments bgcolor = lightslategray fgcolor = black key = Primate protein citation = match:blastx:aa_SPTR.primate category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_vert] feature = match:blastx:aa_SPTR.rodent match:blastx:aa_SPTR.othvert glyph = segments bgcolor = lightslategray fgcolor = black key = Vertebrate protein citation = Blastx rodent, vertebrate aa_SPTR category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } [mb_aa_SPTR.plant] feature = match:blastx:aa_SPTR.plant glyph = segments bgcolor = lightslategray fgcolor = black key = Plant protein citation = match:blastx:aa_SPTR.plant category = ' Blast features' link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//; if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; } elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; } } #--- sim4 features [ms_na_gb.dmel] feature = match:sim4:na_gb.dmel glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel genbank citation = match:sim4:na_gb.dmel category = ' Sim4 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; } [mst_na_gb.dmel] feature = match:sim4tandem:na_gb.dmel glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel genbank (sim4tandem) citation = match:sim4tandem:na_gb.dmel category = ' Sim4 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; } [ms_na_gb.tpa.dmel] feature = match:sim4:na_gb.tpa.dmel glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel genbank tpa citation = match:sim4:na_gb.tpa.dmel category = ' Sim4 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; } [ms_na_transcript_dmel_r32] feature = match:sim4:na_transcript_dmel_r32 glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel r32 transcript citation = match:sim4:na_transcript_dmel_r32 category = ' Sim4 features' link = "#" [ms_na_transcript_dmel_r31] feature = match:sim4:na_transcript_dmel_r31 glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel r31 transcript citation = match:sim4:na_transcript_dmel_r31 category = ' Sim4 features' link = "#" [ms_na_gadfly_dmel_r2] feature = match:sim4:na_gadfly_dmel_r2 glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel r2 transcript citation = match:sim4:na_gadfly_dmel_r2 category = ' Sim4 features' link = "#" [ms_na_smallRNA.dros] feature = match:sim4:na_smallRNA.dros glyph = segments bgcolor = lightslategray fgcolor = black key = Dros smallRNA citation = match:sim4:na_smallRNA.dros category = ' Sim4 features' link = "#" [ms_na_ARGs.dros] feature = match:sim4:na_ARGs.dros glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel ARGs citation = match:sim4:na_ARGs.dros category = ' Sim4 features' link = "#" [ms_na_ARGsCDS.dros] feature = match:sim4:na_ARGsCDS.dros glyph = segments bgcolor = lightslategray fgcolor = black key = Dmel ARGs CDS citation = match:sim4:na_ARGsCDS.dros category = ' Sim4 features' link = "#" #-------- Genome reagents ------------------- # see dgc,est above # keep here so shows at top near BAC track [blast] feature = blast glyph = alignment bgcolor = darkorchid fgcolor = darkorchid bump = 1 label = 1 key = Blast hit height = 8 citation = BLAST alignment hit #category = 'hidden' #hidden = 1 link = "#" [BAC] feature = BAC glyph = extending_arrow no_arrows = 1 base = 0 bgcolor = lightslategray fgcolor = lightslategray linewidth = 2 bump = 1 label = 1 key = Tiling BAC citation = BAC (annotation DB ; Chado) category = ' Genome reagents' link = sub { my $nm= shift->name(); return ($nm)?'http://flybase.org/cgi-bin/fbannq.html?DBX='.$nm : ''; } ## aug04 - was segment; renamed to SO equivalent golden_path ??? [scaffold] feature = scaffold glyph = anchored_arrow no_arrows = 1 base = 0 fgcolor = black bgcolor = black linewidth = 2 bump = 1 label = 1 height = 4 key = GenBank Scaffold citation = golden_path segment (annotation DB ; Chado) category = ' Genome reagents' link = sub { my $nm= shift->name(); return ($nm)?'http://flybase.org/cgi-bin/fbannq.html?ARM='.$nm : ''; } ### feature count table: update w/ fsource grouping # mysql> select count(f.fid),ft.ftypeid,ft.fmethod,ft.fsource # -> from fdata f,ftype ft where f.ftypeid = ft.ftypeid # -> group by ft.fmethod, ft.fsource; # # # +--------------+---------+-------------------------------------+-----------------------------+ # | count(f.fid) | ftypeid | fmethod | fsource | # +--------------+---------+-------------------------------------+-----------------------------+ # | 79 | 70 | aberration_junction | . | # | 674 | 57 | BAC | . | # | 18941 | 31 | CDS | . | # | 6 | 2 | chromosome | . | # | 6 | 7 | chromosome_arm | . | # | 5770 | 3 | chromosome_band | . | # | 6 | 1 | Component | reference | # | 5 | 96 | DNA_motif | . | # | 27 | 84 | enhancer | . | # | 93075 | 12 | exon | . | # | 21634 | 11 | five_prime_UTR | . | # | 14066 | 20 | gene | . | # | 408 | 63 | insertion_site | . | # | 73345 | 34 | intron | . | # | 434 | 5 | match | assembly:path | # | 207911 | 30 | match | blastx:aa_SPTR.dmel | # | 16610 | 51 | match | blastx:aa_SPTR.insect | # | 21451 | 35 | match | blastx:aa_SPTR.othinv | # | 18036 | 37 | match | blastx:aa_SPTR.othvert | # | 11997 | 47 | match | blastx:aa_SPTR.plant | # | 20850 | 33 | match | blastx:aa_SPTR.primate | # | 21644 | 45 | match | blastx:aa_SPTR.rodent | # | 13765 | 41 | match | blastx:aa_SPTR.worm | # | 5593 | 39 | match | blastx:aa_SPTR.yeast | # | 11063 | 94 | match | genie | # | 17811 | 28 | match | genscan | # | 139 | 99 | match | HDP | # | 11758 | 58 | match | repeatmasker | # | 110 | 78 | match | RNAiHDP | # | 1062 | 65 | match | sim4:na_ARGs.dros | # | 984 | 66 | match | sim4:na_ARGsCDS.dros | # | 85910 | 25 | match | sim4:na_dbEST.diff.dmel | # | 169078 | 14 | match | sim4:na_dbEST.same.dmel | # | 6458 | 13 | match | sim4:na_DGC_dros | # | 14249 | 22 | match | sim4:na_gadfly_dmel_r2 | # | 26531 | 8 | match | sim4:na_gb.dmel | # | 2214 | 68 | match | sim4:na_gb.tpa.dmel | # | 98 | 75 | match | sim4:na_smallRNA.dros | # | 19001 | 23 | match | sim4:na_transcript_dmel_r31 | # | 18799 | 24 | match | sim4:na_transcript_dmel_r32 | # | 23748 | 93 | match | sim4tandem:na_gb.dmel | # | 101190 | 49 | match | tblastx:na_agambiae | # | 34107 | 53 | match | tblastx:na_dbEST.insect | # | 263465 | 43 | match | tblastx:na_dpse | # | 295 | 81 | match:tRNAscan-SE | . | # | 434 | 6 | match_part | assembly:path | # | 364002 | 29 | match_part | blastx:aa_SPTR.dmel | # | 37018 | 52 | match_part | blastx:aa_SPTR.insect | # | 52260 | 36 | match_part | blastx:aa_SPTR.othinv | # | 40052 | 38 | match_part | blastx:aa_SPTR.othvert | # | 24905 | 48 | match_part | blastx:aa_SPTR.plant | # | 52032 | 32 | match_part | blastx:aa_SPTR.primate | # | 53213 | 46 | match_part | blastx:aa_SPTR.rodent | # | 32318 | 42 | match_part | blastx:aa_SPTR.worm | # | 11381 | 40 | match_part | blastx:aa_SPTR.yeast | # | 41282 | 95 | match_part | genie | # | 72887 | 27 | match_part | genscan | # | 164 | 100 | match_part | HDP | # | 11758 | 59 | match_part | repeatmasker | # | 9198 | 91 | match_part | repeat_runner_seg | # | 294 | 79 | match_part | RNAiHDP | # | 5621 | 64 | match_part | sim4:na_ARGs.dros | # | 4720 | 67 | match_part | sim4:na_ARGsCDS.dros | # | 158509 | 26 | match_part | sim4:na_dbEST.diff.dmel | # | 347084 | 16 | match_part | sim4:na_dbEST.same.dmel | # | 10821 | 15 | match_part | sim4:na_DGC_dros | # | 57603 | 17 | match_part | sim4:na_gadfly_dmel_r2 | # | 78406 | 9 | match_part | sim4:na_gb.dmel | # | 2260 | 69 | match_part | sim4:na_gb.tpa.dmel | # | 124 | 76 | match_part | sim4:na_smallRNA.dros | # | 86217 | 18 | match_part | sim4:na_transcript_dmel_r31 | # | 89670 | 19 | match_part | sim4:na_transcript_dmel_r32 | # | 68525 | 92 | match_part | sim4tandem:na_gb.dmel | # | 101190 | 50 | match_part | tblastx:na_agambiae | # | 51275 | 54 | match_part | tblastx:na_dbEST.insect | # | 263465 | 44 | match_part | tblastx:na_dpse | # | 295 | 82 | match_part:tRNAscan-SE | . | # | 8 | 74 | mature_peptide | . | # | 16884 | 21 | mRNA | . | # | 140 | 87 | ncRNA | . | # | 197525 | 55 | oligo | . | # | 458 | 71 | point_mutation | . | # | 123 | 73 | polyA_site | . | # | 92 | 85 | protein_binding_site | . | # | 39 | 80 | pseudogene | . | # | 30 | 86 | region | . | # | 137 | 88 | regulatory_region | . | # | 9199 | 90 | repeat_region | . | # | 135 | 62 | rescue_fragment | . | # | 96 | 98 | rRNA | . | # | 437 | 4 | scaffold | . | # | 209 | 72 | sequence_variant | . | # | 1 | 97 | signal_peptide | . | # | 28 | 89 | snoRNA | . | # | 29 | 77 | snRNA | . | # | 16020 | 56 | three_prime_UTR | . | # | 36921 | 10 | transcription_start_site | . | # | 1571 | 61 | transposable_element | . | # | 16404 | 60 | transposable_element_insertion_site | . | # | 295 | 83 | tRNA | . | # +--------------+---------+-------------------------------------+-----------------------------+ # 100 rows in set (7 min 6.01 sec)