[GENERAL] description = ITAG 1 Release: Genomic Annotations adaptor = dbi::cxgn_pg db_args = -db ITAG1_release.genomic plugins = AttributeHiliter reference class = Sequence # Web site configuration info stylesheet = /documents/gbrowse/gbrowse.css buttons = /documents/gbrowse/images/buttons tmpimages = /documents/tempfiles/gbrowse js = /documents/gbrowse/js cachedir = /documents/tempfiles/gbrowse help = /documents/gbrowse # Default glyph settings glyph = generic height = 8 bgcolor = cyan fgcolor = black label density = 25 bump density = 10000 # where to link to when user clicks in detailed view link = AUTO # what image widths to offer image widths = 450 680 980 1550 2400 # default width of detailed view (pixels) default width = 680 upload_tracks section = closed display_settings section = closed # max and default segment sizes for detailed view max segment = 500000 default segment = 50000 # 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 bgcolor = white detailed bgcolor = white key bgcolor = beige language = en # a footer # Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = #html4 =
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html5 = html6 = ### defaults examples sub, works for any of them examples=sub { my ($dbgff) = @_; if($dbgff && $dbgff->can('features_db') ) { my $dbh = $dbgff->features_db; my $examples = $dbh->selectall_arrayref('select fref,seqlen from fdata join (select fref,max(foffset) as seqlen from fdna group by fref having max(foffset) <=500000 order by seqlen desc limit 70) as lens using(fref) group by fref,seqlen order by seqlen desc limit 4 offset 2'); return map $_->[0],@$examples } else { return (); } } ### DAS CONFIGURATION #### das mapmaster = SELF default features = genespan mrna cds aggregators = gappedmatch{match_part/match} eugtranscript{five_prime_UTR,CDS,three_prime_UTR} eugcds{CDS} italymatch{match} # "automatic" classes to try when an unqualified identifier is given automatic classes = Sequence clone match nucleotide_motif ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks #track to show DNA and GC content [DNA] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red category = General axis_color = blue strand = both key = DNA/GC Content citation = This track displays a GC content graph of the reference sequence at low magnifications and the DNA sequence itself at higher magnifications. #track to show a 6-frame translation of the sequence [Translation] glyph = translation global feature = 1 height = 40 fgcolor = purple category = General start_codons = 0 stop_codons = 1 translation = 6frame key = 6-frame translation citation = This track displays a six-frame translation of the reference DNA sequence. [genespan] feature = gene:ITAG_renaming key = Gene span glyph = segments fgcolor = black bgcolor = darkorange stranded = 1 description = sub { use CXGN::Page::FormattingHelpers; CXGN::Page::FormattingHelpers::truncate_string((shift->attributes('functional_description'))[0], 20, '...') } font2color = blue title = sub { (shift->attributes('functional_description'))[0] } category = Gene Model features das category = transcription strand_arrow = 1 height = 10 citation = This track shows the spans of gene models annotated by EuGene, the integrative gene predictor for ITAG. (see EuGene on ITAG Wiki, EuGene main page) [mrna] feature = eugtranscript:ITAG_renaming key = mRNA glyph = processed_transcript fgcolor = black bgcolor = goldenrod stranded = 1 font2color = blue category = Gene Model features das category = transcription strand_arrow = 1 height = 10 citation = This track shows the mRNAs for gene models annotated by EuGene, the integrative gene predictor for ITAG. (see EuGene on ITAG Wiki, EuGene main page) [cds] feature = eugcds:ITAG_renaming key = CDS - click models to browse protein domains title = sub { my $n = shift->display_name; $n =~ s/(mRNA|CDS)://; $n =~ s/(\.\d+)\.\d+$/$1/; "click to browse annotations on $n protein product"} glyph = segments fgcolor = black bgcolor = yellow label = sub { my $n = shift->display_name; $n =~ s/mRNA:/CDS:/; $n } stranded = 1 category = Gene Model features das category = transcription strand_arrow = 1 link = sub { my $n = shift->display_name; $n =~ s/(mRNA|CDS)://; $n =~ s/(\.\d+)\.\d+$/$1/; "/gbrowse/gbrowse/ITAG1_protein/?name=$n" } height = 10 citation = This track shows the CDS sequences for gene models annotated by EuGene, the integrative gene predictor for ITAG. Provided by Stephane Rombauts and Jeffrey Fawcett, Bioinformatics and Evolutionary Genomics, Plant Systems Biology, VIB, Ghent University. (see also EuGene on ITAG Wiki, EuGene main page) [cdna_tom] feature = italymatch:ITAG_transcripts_tomato key = ESTs and cDNAs - Tomato category = Genome data and reagents glyph = segments stranded = 1 link = http://www.ebi.ac.uk/ebisearch/search.ebi?db=nucleotideSequences&t=$name citation = This track shows regions of similarity with EST and other cDNA sequences from Tomato. Provided by CAB group at UNINA. (see ITAG Wiki) [cdna_sol] feature = italymatch:ITAG_transcripts_sol key = ESTs and cDNAs - Other Solanaceae category = Genome data and reagents glyph = segments stranded = 1 link = http://www.ebi.ac.uk/ebisearch/search.ebi?db=nucleotideSequences&t=$name citation = This track shows regions of similarity with EST and other cDNA sequences taken from species in the Solanaceae other than Tomato. Provided by CAB group at UNINA. (see ITAG Wiki) [sgn_unigenes] feature = match:ITAG_sgn_unigenes key = SGN Unigenes category = Genome data and reagents glyph = segments stranded = 1 link = http://sgn.cornell.edu/search/quick_search.pl?term=$name citation = This track shows regions of similarity with SGN Unigene (SGN-U) sequences. (see ITAG Wiki) [augustus] feature = processed_transcript: key = AUGUSTUS (de novo, Tomato trained) category = Prediction Features glyph = processed_transcript stranded = 1 citation = De novo gene predictions from the AUGUSTUS gene predictor, trained on Tomato. Provided by SGN. (see ITAG Wiki) [geneid_tomato] feature = processed_transcript:ITAG_geneid_tomato key = GeneID (de novo, Tomato trained) category = Prediction Features glyph = processed_transcript stranded = 1 citation = De novo predictions from GeneID, trained on Tomato. Provided by Francisco Camara, Genome Bioinformatics Research Lab - Gene Prediction Group, Center for Genomic Regulation (CRG) - Spain. (see also ITAG Wiki) [genemark_ath] feature = processed_transcript:ITAG_genemark_ath key = GeneMark (de novo, Arabidopsis trained) category = Prediction Features glyph = processed_transcript stranded = 1 citation = De novo predictions from GeneMark, trained on Arabidopsis. Provided by the MIPS Tomato genome database. (see also ITAG Wiki) [glimmerhmm_ath] feature = processed_transcript:ITAG_glimmerhmm_ath key = GlimmerHMM (de novo, Arabidopsis trained) category = Prediction Features glyph = processed_transcript stranded = 1 citation = De novo predictions from GlimmerHMM, trained on Arabidopsis. Provided by Erwin Datema at WUR. (see also ITAG Wiki) [glimmerhmm_tomato] feature = processed_transcript:ITAG_glimmerhmm_tomato key = GlimmerHMM (de novo, Tomato trained) category = Prediction Features glyph = processed_transcript stranded = 1 citation = De novo predictions from GlimmerHMM, trained on Tomato. Provided by Erwin Datema at WUR. (see also ITAG Wiki) [infernal] feature = snoRNA:ITAG_infernal U6atac_snRNA:ITAG_infernal miRNA:ITAG_infernal antisense_RNA:ITAG_infernal snRNA:ITAG_infernal 5_snRNA:ITAG_infernal 13_snRNA:ITAG_infernal 10_snRNA:ITAG_infernal snRNA:ITAG_infernal 11_snRNA:ITAG_infernal 6_snRNA:ITAG_infernal snoRNA:ITAG_infernal 12_snRNA:ITAG_infernal U1_snRNA:ITAG_infernal group_I_intron:ITAG_infernal 7_snRNA:ITAG_infernal UTR_region:ITAG_infernal group_II_intron:ITAG_infernal miRNA:ITAG_infernal SRP_RNA:ITAG_infernal snRNA:ITAG_infernal snoRNA:ITAG_infernal 14_snRNA:ITAG_infernal 4_snRNA:ITAG_infernal miRNA:ITAG_infernal U2_snRNA:ITAG_infernal 9_snRNA:ITAG_infernal rRNA_5.8S:ITAG_infernal 8_snRNA:ITAG_infernal RNAi_reagent:ITAG_infernal key = Infernal category = Prediction Features glyph = segments stranded = 1 citation = This track shows RNA regions inferred by Infernal. Provided by Daniel Buchan, SRCUK. [trnascanse] feature = tRNA:ITAG_trnascanse key = tRNAscanSE category = Prediction Features glyph = segments stranded = 1 citation = This track shows transfer RNAs predicted by the tRNAscan-SE program. For more on tRNAscan-SE, see http://selab.janelia.org/software#trnascanse. (see also ITAG Wiki) [sgn_loci] feature = match:ITAG_sgn_loci key = SGN Locus Sequences category = Genetic Loci glyph = segments link = /search/quick_search.pl?term=$name stranded = 1 citation = This track shows regions of similarity of Eugene-predicted cDNA sequences with known sequences associated with SGN genetic loci, as detected by BLAT (see also ITAG Wiki) #[markers:overview] #feature = match:ITAG_sgn_markers #fgcolor = black #bgcolor = yellow #key = Genetic Markers #glyph = generic [sgn_markers] feature = match:ITAG_sgn_markers key = SGN Marker Sequences category = Genetic Loci stranded = 1 fgcolor = black bgcolor = yellow stranded = 1 citation = This track shows regions of similarity of the genomic sequence with known sequences associated with SGN genetic markers, as detected by GenomeThreader (see also ITAG Wiki)