[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 = <div style="border: 1px solid red; padding: 4px"><b>Troubleshooting tip:</b> if the browser seems to be acting strangely, try hitting the <a class="reset_button" href="?reset=1"><b>[Reset]</b></a> link.</div>
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 <a href="http://www.ab.wur.nl/TomatoWiki/AnEugene000">EuGene on ITAG Wiki</a>, <a href="http://www.inra.fr/internet/Departements/MIA/T//EuGene/index.html">EuGene main page</a>)

[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 <a href="http://www.ab.wur.nl/TomatoWiki/AnEugene000">EuGene on ITAG Wiki</a>, <a href="http://www.inra.fr/internet/Departements/MIA/T//EuGene/index.html">EuGene main page</a>)

[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, <a class="http" href="http://bioinformatics.psb.ugent.be/">Bioinformatics and Evolutionary Genomics</a>, <a class="http" href="http://www.psb.ugent.be">Plant Systems Biology, VIB, Ghent University</a>.  (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnEugene000">EuGene on ITAG Wiki</a>, <a href="http://www.inra.fr/internet/Departements/MIA/T//EuGene/index.html">EuGene main page</a>)

[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 <a href="http://cab.unina.it/index2.php">CAB group</a> at <a href="http://www.unina.it">UNINA</a>. (see <a href="http://www.ab.wur.nl/TomatoWiki/AnEST000">ITAG Wiki</a>)

[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 <a href="http://cab.unina.it/index2.php">CAB group</a> at <a href="http://www.unina.it">UNINA</a>. (see <a href="http://www.ab.wur.nl/TomatoWiki/AnEST000">ITAG Wiki</a>)

[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 <a href="http://www.ab.wur.nl/TomatoWiki/AnSgnUnigenes000">ITAG Wiki</a>)

[augustus]
feature      = processed_transcript:
key          = AUGUSTUS (de novo, Tomato trained)
category     = Prediction Features
glyph        = processed_transcript
stranded     = 1
citation      = <i>De novo</i> gene predictions from the AUGUSTUS gene predictor, trained on Tomato.  Provided by SGN.  (see <a href="http://www.ab.wur.nl/TomatoWiki/AnAUGUSTUS000">ITAG Wiki</a>)

[geneid_tomato]
feature      = processed_transcript:ITAG_geneid_tomato
key          = GeneID (de novo, Tomato trained)
category     = Prediction Features
glyph        = processed_transcript
stranded     = 1
citation     = <i>De novo</i> predictions from <a href="http://genome.imim.es/software/geneid/">GeneID</a>, trained on Tomato.  Provided by Francisco Camara, <a href="http://genome.crg.es">Genome Bioinformatics Research Lab - Gene Prediction Group, Center for Genomic Regulation (CRG) - Spain</a>. (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnGeneID000">ITAG Wiki</a>)

[genemark_ath]
feature      = processed_transcript:ITAG_genemark_ath
key          = GeneMark (de novo, Arabidopsis trained)
category     = Prediction Features
glyph        = processed_transcript
stranded     = 1
citation     = <i>De novo</i> predictions from <a href="http://exon.gatech.edu/GeneMark/">GeneMark</a>, trained on Arabidopsis.  Provided by the <a href="http://mips.gsf.de/proj/plant/jsf/tomato/index.jsp">MIPS Tomato genome database</a>. (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnGeneMark000">ITAG Wiki</a>)

[glimmerhmm_ath]
feature      = processed_transcript:ITAG_glimmerhmm_ath
key          = GlimmerHMM (de novo, Arabidopsis trained)
category     = Prediction Features
glyph        = processed_transcript
stranded     = 1
citation     = <i>De novo</i> predictions from <a href="http://www.genomics.jhu.edu/GlimmerHMM/">GlimmerHMM</a>, trained on Arabidopsis.  Provided by Erwin Datema at <a href="http://appliedbioinformatics.wur.nl/">WUR</a>. (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnGlimmerHMM000">ITAG Wiki</a>)

[glimmerhmm_tomato]
feature      = processed_transcript:ITAG_glimmerhmm_tomato
key          = GlimmerHMM (de novo, Tomato trained)
category     = Prediction Features
glyph        = processed_transcript
stranded     = 1
citation     = <i>De novo</i> predictions from <a href="http://www.genomics.jhu.edu/GlimmerHMM/">GlimmerHMM</a>, trained on Tomato.  Provided by Erwin Datema at <a href="http://appliedbioinformatics.wur.nl/">WUR</a>. (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnGlimmerHMM000">ITAG Wiki</a>)

[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 <a href="http://infernal.janelia.org/">Infernal</a>.  Provided by Daniel Buchan, <a href="http://www.srcuk.org/">SRCUK</a>.

[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 <a href="http://selab.janelia.org/software#trnascanse">http://selab.janelia.org/software#trnascanse</a>.  (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnTRNAScanSE000">ITAG Wiki</a>)

[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 <a href="http://www.ab.wur.nl/TomatoWiki/AnSGNLoci000">ITAG Wiki</a>)

#[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 <a href="http://www.ab.wur.nl/TomatoWiki/AnSgnMarkers000">ITAG Wiki</a>)

