[GENERAL]
description = ITAG 1 Release: Protein Annotations
adaptor  = dbi::cxgn_pg
db_args  = -db ITAG1_release.protein

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 =

aggregators =

# "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
[peptides]
glyph          = protein
global feature = 1
height         = 40
do_gc          = 1
fgcolor        = red
category       = General
axis_color     = blue
strand         = both
key            = Peptides/KD Plot
citation       = This track displays a Kyte-Doolittle hydropathy plot of the protein sequence at low magnifications and the peptide sequence itself at higher magnifications.

[blastp_trembl]
feature      = match:ITAG_blastp_trembl
key          = TrEMBL
category     = Similarity
glyph        = segments
stranded     = 1
citation     = This track shows similarities with sequences in TrEMBL (see <a href="http://www.ebi.ac.uk/trembl/">http://www.ebi.ac.uk/trembl/</a>), as detected by BLAST (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnBlastP000">ITAG Wiki</a>)
bgcolor      = lightgreen

[blastp_refseq_pep]
feature      = match:ITAG_blastp_refseq_pep
key          = RefSeq Peptides
category     = Similarity
bgcolor      = lightgreen
glyph        = segments
stranded     = 1
citation     = This track shows similarities with peptide sequences in RefSeq (see <a href="http://www.ncbi.nlm.nih.gov/RefSeq/">http://www.ncbi.nlm.nih.gov/RefSeq/</a>), as detected by BLAST (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnBlastP000">ITAG Wiki</a>)

[blastp_rice_pep]
feature      = match:ITAG_blastp_rice_pep
key          = Rice Peptides
category     = Similarity
bgcolor      = cyan
glyph        = segments
stranded     = 1
citation     = This track shows similarities with Rice peptide sequences from RAP-DB (see <a href="http://rapdb.dna.affrc.go.jp/rapdownload/">http://rapdb.dna.affrc.go.jp/rapdownload/</a>), as detected by BLAST (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnBlastP000">ITAG Wiki</a>)

[blastp_swissprot]
feature      = match:ITAG_blastp_swissprot
key          = SwissProt
category     = Similarity
bgcolor      = lightgreen
glyph        = segments
stranded     = 1
citation     = This track shows similarities with peptide sequences in SwissProt (see <a href="http://www.expasy.ch/sprot/">http://www.expasy.ch/sprot/</a>), as detected by BLAST (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnBlastP000">ITAG Wiki</a>)

[blastp_ath_pep]
feature      = match:ITAG_blastp_ath_pep
key          = Arabidopsis Peptides
category     = Similarity
glyph        = segments
bgcolor      = cyan
stranded     = 1
citation     = This track shows similarities with peptide sequences from <i>Arabidopsis thaliana</i> (see <a href="ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR8_blastsets">ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR8_blastsets</a>), as detected by BLAST (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnBlastP000">ITAG Wiki</a>)

[interpro]
feature      = polypeptide_region:ITAG_interpro
key          = Interpro
bgcolor      = blue
category     = Protein Domain Similarities
glyph        = segments
stranded     = 1
citation     = Protein domains found by Interproscan (see also <a href="http://www.ab.wur.nl/TomatoWiki/AnInterpro000">ITAG Wiki</a>)

[rpsblast]
feature      = match:ITAG_rpsblast
key          = RPS-BLAST
bgcolor      = lightblue
category     = Protein Domain Similarities
glyph        = segments
stranded     = 1
citation     = Protein domain matches found by RPS-BLAST (see <a href="http://www.ab.wur.nl/TomatoWiki/AnRPSBlast000">ITAG Wiki</a>)

