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Drosophila ananassae
# lucegene GFF adaptor db_adaptor = Bio::DB::GFF db_args = -adaptor lucene -dsn ../databases/drospege/dana_caf060210;dana_caf1an4;dana_caf1an4d;dana_est default_name = scaffold_1:1..50000 default_range = 1-500000 # examples to show in the introduction examples = scaffold_1:1..50000 ci Mad eve run jim loco odd stan can rut tin toy ## need this for Chado segment lookup in Browser.pm _feature_get ... ## reference class = scaffold # Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = ########## COMMON DROSPEGE GBROWSE.CONF ################# aggregators = processed_transcript processed_transcript2 alignment nucleotide_match{match_part/match} protein_match{match_part/match} estmatch{match_part/EST_match} tRNAgene{exon/tRNA} # stemloop is missing from ggb169 aggrs ? default features = hsgDM EST OLIVEXP NCBIGNO PACHGMP OXFDGPI EISECGW DGILSNO BRENNSC RGUIGID BATZCNA EISEGLR ReAS uploads = 1 no uploads = 0 # Web site configuration info; urk FIXME ... installer gbrowse root = gbrowse stylesheet = gbrowse.css buttons = images/buttons js = js tmpimages = tmp # region segment = 100000 # advanced features balloon tips = 0 drag and drop = 1 cache time = 1 # one hour # popup balloon configuration; 'balloon' is the default # custom balloons = # [balloon] # images = /gbrowse/images/balloons # [balloon375] # images = /gbrowse/images/balloons # maxWidth = 375 # delayTime = 200 footer =| See the Generic Model Organism Database Project. |
plugins = BatchDumper FastaDumper GFFDumper ProteinDumper # FeatureFastaDumper # max and default segment sizes for detailed view max segment = 1000001 default segment = 100000 # low-res boundary low res = 200000 zoom levels = 100 200 1000 2500 5000 10000 25000 50000 75000 100000 150000 200000 300000 500000 1000000 searchhelp = Search using Chromosome:base_start..end or Gene name/ID. # # where to link to when user clicks in detailed view link = AUTO title = sub { my $f= shift; my $loc= $f->seq_id .':'.$f->start."..".$f->end; my $ftype= ($f->can("method")) ? $f->method : $f->type; if ($ftype =~ /^match/) { $ftype= $f->source(); } my $nm; if($f->can("attributes")) { ($nm)= grep( /^\w/, $f->attributes('Name'), $f->attributes('Alias'), $f->attributes('symbol'), $f->attributes('name'), $f->attributes('ID'), $f->name); } else { $nm= $f->display_name(); } if($f->can("score")) { my $sc= $f->score; $nm .= " p=$sc" if ($sc =~ /\d/); } return "$ftype:$nm $loc"; } ## 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/:/,$x,2; if ($db eq 'GB_protein') { $v= $ac; $h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenBank&tool=GMOD&term='.$ac; } elsif ($db eq 'GB') { $v= $ac; $h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=GMOD&term='.$ac; } elsif ($db eq 'GO') { $v= $ac; $h= '/cgi-bin/goreport?id='.$ac; } if ($h && $v) { $r.= ''.$v.', '; } else { $r.= $x.', '; } } return $r; } #panel property pad_left = 20 pad_right = 30 key_style = between grid = 1 # put reversed features on same track or below ? mix_strand = 1 # 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 = match language = en image widths = 450 640 800 950 1024 default width = 800 # Advanced feature: an example of callback to be run remotely # by gbrowse_details for AJAX/iframe balloons # [TOOLTIPS] # intro = sub { # my $args = shift; # my $feat = $args->{feature}; # #my $name = $feat->display_name; # my($name)= ( $feat->attributes('Name'), $feat->display_name()); # my $type = $feat->primary_tag; # # my $class = $feat->class; # my $class = $feat->source; # my $extra = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note'); # my $n = $type =~ /^[AEIOU]/i ? 'n' : ''; # my $msg = "Hello, I am $name, a$n $type from $class"; # $msg .= "
Note: $extra
" if $extra; # #my $seq = substr $feat->seq->seq, 0, 400; # #$seq =~ s/(\S{50})/$1\n/g; # return "
| $name |
|---|
| $msg |
";
# # "First 400 bp (click on $type $name for the full sequence):".
# # ">$name\n$seq |
>$name\n$seq"; # } ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [BatchDumper:plugin] fileformat = embl [GFFDumper:plugin] version = 3 [ProteinDumper:plugin] fileformat = embl [TRACK DEFAULTS] glyph = generic height = 6 label density = 20 bump density = 50 overview label density = 160 #balloon hover = $name $type at $ref:$start..$end [hsgDM] feature = alignment:modDM glyph = merged_alignment bins = 0-50 50-100 100-200 200-9000 bincolors = #A0A0A0 powderblue cornflowerblue blue stranded = 1 height = 5 category = Analysis key = Fruitfly protein HSPs citation = D.melanogaster protein tBLASTn matches, grouped by HSP overlap. Names are protein ID + HSP group. To see all HPS groups, search with "ID_*" in Landmark. ID Key: CG00000_G1 = primary Gene match (best hit), CG0000_G2 = secondary Gene match on same scaffold, CG0000_S[3..n] = tertiary and further matches of same protein on same scaffold as _G1, CG0000_o[1..n] = further matches on other scaffolds. Matches at p <= 1e-3 are collected, secondary matches that mostly overlap better matches are removed. HSPs are grouped by both protein fragment overlap (same part of protein?) and target genome overlap. HSP groups include several gene events: alternate splice exons in same gene, tandem and distant duplications, new genes composed of parts of several other genes, as well as computational artifacts. See here for further details and use in Gene Ontology groups D. Gilbert, may 06 label = sub { my $f = shift; my($na)= ( $f->attributes('Parent'), $f->display_name()); return $na; } [blastndmel] feature = cross_genome_match:dmelchr glyph = segments stranded = 1 height = 5 bgcolor = lightslategray fgcolor = black key = D.mel chromosomes citation = D.mel chromosomes category = Genome features link = sub { my $f= shift; ## Target isn't attribute; bioperl puts into ? group() target() my ($t)= $f->attributes('Target'); if ($t) { $t=~s/^\w+://; $t=~s/[\s+]/:/; $t=~s/[\s+]/../; return '/species/cgi-bin/gbrowse/dros_spp/?name='.$t; } $t= $f->target(); if ($t) { my ($tn,$tb,$te)= ($t->name(),$t->start(), $t->stop()); return "/species/cgi-bin/gbrowse/dros_spp/?name=$tn:$tb..$te"; } } [markers] feature = match:marker:modDM bgcolor = green glyph = segments stranded = 1 key = Dmel. marker citation = Dmel. marker category = Analysis #label = sub { my $f= shift; # my ($nm)= ( $f->display_name() ); # default works for markers, ID=gene-name # return $nm; # } [blastdmic] feature = nucleotide_match:blastn:drosmicsat glyph = segments stranded = 1 bgcolor = lavender fgcolor = black key = Drosophila microsatellites citation = Drosophila microsatellites category = Analysis label = sub { my $f = shift; my @na= ($f->attributes('Name'), $f->attributes('Alias'), $f->attributes('symbol')); return $na[0] || $f->display_name; } link = sub { my($ac) = shift->attributes('ID'); $ac =~ s/[\.\|].*$//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=GMOD&term='.$ac if ($ac); } [hsgCE] feature = alignment:modCE glyph = merged_alignment bins = 0-50 50-100 100-200 200-9000 bincolors = #A0A0A0 powderblue cornflowerblue blue stranded = 1 height = 5 category = Analysis key = C.elegans protein HSPs label = sub { my $f = shift; my($na)= ( $f->attributes('Parent'), $f->display_name()); return $na; } [hsgMM] feature = alignment:modMM glyph = merged_alignment bins = 0-50 50-100 100-200 200-9000 bincolors = #A0A0A0 powderblue cornflowerblue blue stranded = 1 height = 5 category = Analysis key = Mouse protein HSPs label = sub { my $f = shift; my($na)= ( $f->attributes('Parent'), $f->display_name()); return $na; } [hsgSC] feature = alignment:modSC glyph = merged_alignment bins = 0-50 50-100 100-200 200-9000 bincolors = #A0A0A0 powderblue cornflowerblue blue stranded = 1 height = 5 category = Analysis key = Yeast protein HSPs label = sub { my $f = shift; my($na)= ( $f->attributes('Parent'), $f->display_name()); return $na; } [dna] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red axis_color = blue nodump = 1 category = Genome features key = DNA/GC Content ########## END COMMON DROSPEGE GBROWSE.CONF ################# [processed_transcript:DETAILS] Type = sub { my ($val,$tag,$f) = @_; my $surl= "../gbrowse/dana/"; ## fixme, get from selfurl : CGI::url() ?? my $fid= $f->display_name(); ##not id(); my $furl= $surl."\?name=$fid;pid=1;plugin=ProteinDumper;plugin_do=1"; return $val . " ( Get Protein )"; } ######## COMMON prediction trax GBROWSE.CONF ################# ## EST works when gffloader skips Target: load_gff -group 'Parent ID' [EST] feature = estmatch:BLAT #glyph = transcript2 glyph = segments stranded = 1 bgcolor = #c0f0d0 fgcolor = black key = EST category = Analysis [Name:DETAILS] URL = sub { my($tag,$d)= @_; #warn "tag:details args:",join(",",@_),"\n"; if ($d =~ /_mid/) { my $fid= $d; $fid =~ s,\,,g; $fid =~ s/_\w+$//; # _midN tag ; doptcmdl GenBank or EST my $ncbi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi'; return $ncbi.'?cmd=Search&db=nucest&doptcmdl=GenBank&tool=GMOD&term='.$fid; } } # for dana,dmoj,dvir,dpse,dsim,dyak in lucene index dXXX_caf1an3 [OLIVEXP] feature = mRNA:OLIV_EXP glyph = transcript2 stranded = 1 height = 4 key = Expression data: OLIV_EXP citation = Array expression data Dave Sturgill (davidsturgill@niddk.nih.gov), Yu Zhang, Michael Parisi, and Brian Oliver. LCDB/NIDDK/NIH more info category = Analysis label = 0 old_label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [NCBIGNO] feature = processed_transcript:NCBI_GNO glyph = processed_transcript bgcolor=lightpink thin_utr = 1 key = Gnomon: NCBI_GNO citation = Gnomon predictions of Alexander Souvorov, Wratko Hlavina, Yuri Kapustin, Boris Kiryutin, Paul Kitts, Kim Pruitt, Victor Sapojni kov and Jim Ostell http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.html category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [PACHGMP] # exon, CDS parts feature = processed_transcript:PACH_GMP glyph = processed_transcript bgcolor=mediumaquamarine thin_utr = 1 key = GeneMapper: PACH_GMP citation = GeneMapper (ver 1.9 beta) predictions of Sourav Chatterji and Lior Pachter category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [OXFDGPI] # gene, exon, CDS parts feature = processed_transcript2:OXFD_GPI processed_transcript:OXFD_GPX glyph = processed_transcript bgcolor=lightcoral thin_utr = 1 key = Oxford pipeline: OXFD_GPI citation = Oxford gene prediction pipeline based on the program exonerate. Andreas Heger and Chris Ponting at firstname.lastname@anat.ox.ac.uk category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); my ($nt)= ($f->attributes('class')); $na.=" ($nt)" if($nt); $na =~ s/scaffold_/s/; return $na; } [EISECEX] # gene, exon, intron, splice_donor_site, splice_acceptor_site parts feature = processed_transcript2:EISE_CEX glyph = processed_transcript bgcolor=lightsteelblue thin_utr = 1 key = Exonerate: EISE_CEX citation = Exonerate predictions of Venky N. Iyer, Daniel A. Pollard and Michael B. Eisen category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [EISECGM] # exon, CDS parts feature = processed_transcript:EISE_CGM glyph = processed_transcript bgcolor=lightsteelblue thin_utr = 1 key = GeneMapper: EISE_CGM citation = GeneMapper predictions of Venky N. Iyer, Daniel A. Pollard and Michael B. Eisen category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [EISECGW] # exon, CDS parts feature = processed_transcript:EISE_CGW glyph = processed_transcript bgcolor=lightsteelblue thin_utr = 1 key = GeneWise: EISE_CGW citation = GeneWise predictions of Venky N. Iyer, Daniel A. Pollard and Michael B. Eisen category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [DGILSNP] # gene, exon parts feature = processed_transcript2:DGIL_SNP glyph = processed_transcript bgcolor=mediumturquoise thin_utr = 1 key = SNAP: DGIL_SNP citation = SNAP gene predictor (v. 2005-07-27) of Don Gilbert, http://insects.eugenes.org/DroSpeGe/data/ category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [DGILSNO] feature = processed_transcript2:DGIL_SNO glyph = processed_transcript bgcolor=mediumturquoise thin_utr = 1 key = SNAP_hsp: DGIL_SNO citation = SNAP gene predictor + protein homology (v. 2006-05) of Don Gilbert, http://insects.eugenes.org/DroSpeGe/data/ category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [RGUIGID] # gene, exon, CDS parts ? feature = processed_transcript:RGUI_GID glyph = processed_transcript bgcolor=lightsalmon thin_utr = 1 key = geneid: RGUI_GID citation = geneid [version ...] predictions with no alignment information by [citation here] category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [BRENNSC] # gene, exon, CDS parts ? feature = processed_transcript:BREN_NSC glyph = processed_transcript bgcolor=mediumspringgreen thin_utr = 1 key = N-SCAN: BREN_NSC citation = N-Scan [version ...] predictions using homology information by [citation here] category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [BATZCNA] # CDS parts feature = processed_transcript:BATZ_CNA glyph = processed_transcript bgcolor=mediumseagreen thin_utr = 1 key = Contrast: BATZ_CNA citation = CONTRAST predictions with no alignment information by Samuel S. Gross, Chuong B. Do, Marina Sirota, and Serafim Batzoglou category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } ## 17jul06 add [EISEGLN] # mRNA,CDS parts feature = processed_transcript:GLEAN glyph = processed_transcript bgcolor=salmon thin_utr = 1 key = Glean: EISE citation = Glean prediction combiner software by A. Mackey et al, generation by Venky N. Iyer category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } [UMDJIG] # mRNA,CDS parts feature = processed_transcript:JIGSAW glyph = processed_transcript bgcolor=lightsteelblue thin_utr = 1 key = Jigsaw: UMD citation = Jigsaw prediction combiner by category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } ## 15aug06 dsn add: [EISEGLR] # mRNA,CDS parts feature = processed_transcript:GLEANR glyph = processed_transcript bgcolor=gold thin_utr = 1 key = GleanR: EISE citation = Glean [R] prediction combiner using various data partitions and selections software by A. Mackey et al, generation by Venky N. Iyer category = Prediction label = sub { my $f = shift; my ($na)= ($f->attributes('Name'), $f->display_name); $na =~ s/scaffold_/s/; return $na; } # 23aug06: DGIL_TEX taxonomically validated Dmel exons # NOTE: this is match:DGIL_TEX except for dmel = CDS:DGIL_TEX [DGILTEX] feature = match:DGIL_TEX stranded = 1 glyph = segments bgcolor = green key = New Dmel exons citation = Taxonomically identified new Dmel coding exons DGIL_TEX by D. Gilbert category = Prediction ## nov06: fixme to show scores of repeats ReAS ? [ReAS] feature = repeat_region:ReAS glyph = segments bgcolor = wheat fgcolor = black stranded = 1 height = 5 bump = 0 label = 0 category = Analysis key = Transposon Repeats: ReAS citation = ReAS v2 de novo repeat assembly based on raw sequencing reads URL: ftp://ftp.genomics.org.cn/pub/reas/drosophila/v2/ AUTHORS: Ruiqiang Li, Gane Ka-Shu Wong and Jun Wang CONTACT: lirq@genomics.org.cn GROUP: BGI, Beijing Genomics Institute, Beijing, China. REFERENCE: Li R, Ye J, Li S, Wang J, Han Y, et al (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4): e43. # aggregators: tRNAgene{exon/tRNA} stemloop ## various parent/child (exon) RNAs; source is 'ncRNA' for all [ncRNA] feature = tRNAgene stemloop:ncRNA snoRNA rRNA_5S rRNA_5.8S SRP_RNA SECIS_element RNase_P_RNA RNA_sequence_secondary_structure U1_snRNA U2_snRNA U4_snRNA U5_snRNA U6_snRNA riboswitch group_I_intron group_II_intron #glyph = segments glyph = transcript bgcolor = lightsteelblue category = Prediction key = ncRNA citation = ncRNA reconciled (Nov.06) from annotation-group: RFAM + TRNA_ATT algorithm: INF, MIR, BLASTN, Aragorn+tRNAscan-SE->TFAM authors: sgj[at]sanger.ac.uk, jd7[at]sanger.ac.uk, casey.bergman[at]manchester.ac.uk, dave.ardell[at]lcb.uu.se
