worm_japonica.conf

#C.japonica main config


[GENERAL]
description     = C. japonica modENCODE (WormBase build WS227)
database        = japonicaWS227
category default state = closed
category default state = closed
category state  = "Gene Structure" open
                  "RNA Expression Profiling" open
                   Analysis open
category tables = 'Gene Structure:Gene Models:Confirmed Sites' 'Introns PolyA SpliceLeaders' 'EarlyEmbryo L2 L4 AdultFemale AdultMale.Rep.1'

initial landmark = Cjap.Contig1:10000..19000

default features = Genes

# examples to show in the introduction
examples = Cjap.Contig2:2000..12000
           Cjap.Contig4:1500..8000


header =
  <table style="border-bottom:5px groove blue;margin-bottom:10px;width:98%">
    <tr>
      <td valign=top width=80>
       <a href="http://www.modencode.org">
         <img src="/images/modENCODE_logo_tiny.png"
              border=0 alt="modENCODE logo" />
       </a>
      </td>
      <td valign=top>
        <a href="http://modencode.oicr.on.ca/gb2/gbrowse/fly">
          <img src="/images/fly_small.png"
               border=0 alt="modENCODE logo fly" />
        </a>
      </td>
      <th valign=middle>
        <span style="font:arial;font-size:18pt"><i>C. japonica</i> Genome Browser</span>
      </th>
      <td width="20%"></td>
    </tr>
  </table>

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Gene Operon Genbank Variation Allele CDS Transposon Sequence Clone
pad_left          = 250
image_padding     = 100
truecolor         = 1
autocomplete      = 1
seqid_prefix      = chr
#galaxy outgoing   = http://main.g2.bx.psu.edu/tool_runner?tool_id=modENCODEworm
# galaxy outgoing = http://modencode.oicr.on.ca/cgi-bin/mock_galaxy


#################################
# database definitions
#################################

[japonicaWS227:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    japonicaWS227
                -user   nobody
search options = default +autocomplete


[waterston_japon:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    waterston_japon
                -user   nobody
search options = exact


# Default glyph settings
[TRACK DEFAULTS]
glyph         = generic
database      = japonicaWS227
height        = 8
bgcolor       = lightgrey
fgcolor       = black
label density = 100
bump density  = 500
feature_limit = 500
link          = AUTO
show summary  = 1000000
discoverable  = 1

#MotifFinder plugin configuration
#[MotifFinder:plugin]
#matrix = matrices.txt

#Ucsc plugin configuration
#[UcscPlugin:plugin]
#db = ce6
#user = viewer
#pass = viewer
#seq_prefix = chr
#split_prefix = chr

#[UcscChain:plugin]
#default_enable = chainCb3

#[UcscNet:plugin]
#default_enable = netCb3 netCaeRem3

#[UcscConservation:plugin]
#default_enable = multiz6way
#citation       = The UCSC Conservation plugin shows a measure of evolutionary conservation in multiple species, based on a phylogenetic hidden Markov model, 
# phastCons (Siepel et al., 2005). phastCons uses a phylogenetic tree and multi-species alignments. 
# Pairwise alignments are generated using blastz, chaining and netting, and multiz joins the pairwise alignments into multiple alignments.
# In full and pack display modes, conservation scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. Pairwise alignments of each species to the worm genome are displayed below as a grayscale density plot (in pack mode) or as a "wiggle" (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.<br/><br/><a href="http://genome.ucsc.edu/cgi-bin/hgc?g=multiz6way">Ucsc Website</a>
#link  = ftp://hgdownload.cse.ucsc.edu/gbdb/ce6/multiz6way/anno/maf/

### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks

[Genes:1000000]
bgcolor      = gray

[Genes:100000]
glyph        = generic
bump         = 0
maxdepth     = 1
stranded     = 1
label        = 0
description  = 0


[Genes]
feature      = CDS:Coding_transcript
glyph        = gene
bgcolor      = sub {my $f = shift;
                    return 'white' if $f->primary_tag eq 'pseudogene';
                    return $f->strand < 1 ? 'turquoise' : 'violet';
                    }
fgcolor      = black
strand_arrow = 1
#strand_arrow = sub {my $f = shift;
#                    return $f->primary_tag eq 'pseudogene';}
forwardcolor = violet
reversecolor = cyan
utr_color    = gray
category     = Annotations for Curated and Predicted Genes from WormBase
height       = sub {shift->primary_tag eq 'pseudogene' ? 6 : 8;}
label        = sub {my $f = shift;
                my $dn = $f->load_id =~ /^Gene/? $f->display_name : $f->load_id;
                $dn =~ s/Transcript://;
                my @aliases = $f->each_tag_value('Note');
                foreach (@aliases) {
                   return lc($1)." ($dn) " if /(\w{3,4}-\d+)$/;
                }
                return $dn;
               }
link         = sub{my $name = shift->load_id;
                   $name=~s/CDS\://; 
                   return qq[ http://www.wormbase.org/db/gb2/gbrowse/c_japonica/?name=$name];}
label_transcripts =  1
das category = transcription
key          = Curated WormBase Genes
sort_order   = name
citation     = <h1>C.japonica WS227</h1>
	     <br>
             These are gene predictions that have been reviewed by WormBase curators.  The
             purple and blue colors indicate CDS regions on the forward and
             reverse strands respectively.  The grey areas represent 5' and
             3' ESTs assigned automatically using the extents of
             overlapping ESTs and full-length cDNAs.  The UTR predictions
             have <b>not</b> been reviewed by WormBase curators, and are
             known to contain artifacts. If sufficient room is available
             between features, gene models end with a triangle; if not a
             small arrow is used.  The tRNAs are predicted by Sean Eddy's
             tRNAscan program, and miRNA transcripts taken from a variety
             of literature sources. RNAz-derived ncRNAs were predicted using
             the <a href="http://www.tbi.univie.ac.at/~wash/RNAz/">RNAz algorithm</a>.
             Please select the RNA for more details.
title        = Curated wormbase gene $name



#[NCRNA]
#feature           = ncRNA:ncRNA
#database          = japonicaWS227
#filter            = sub {
#                      my @subf = eval{shift->get_SeqFeatures};
#		      return grep {!/mRNA|tRNA/} @subf;
#		      }
#glyph            = generic
#strand_arrow     = 1
#bgcolor          = sub {return shift->strand < 1 ? 'orange' : 'wheat';}
#fgcolor          = black
#height           = 5
#description      = 1
#key              = Non-coding RNAs
#label            = sub{
#                       my $f = shift;
#		       my $dn = $f->display_name;
#		       $dn =~ s/Transcript://;
#		       my @aliases = $f->each_tag_value('Note');
#		       foreach (@aliases) {
#		              $dn = $_;
#		              return "$1 " if /(\w{3}-\d+)$/;
#		       }
#		       return $dn;
#		       }
#label_transcripts =  1
#category         = Annotations for Curated and Predicted Genes from WormBase
#citation         = noncoding RNAs, including snRNAs, snoRNA, miRNAs, ncRNAs and rRNAs. Extent of transcribed region corresponding
#		   to an annotated non-coding RNA (intron structure not shown)
#
#               Gene models are available for download at ftp://ftp.wormbase.org/pub/wormbase/nGASP/final_gene_predictions/predictions


[TranslationF]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = purple
start_codons = 0
strand       = +1
arrow_height = 2
translation  = 3frame
category     = non-modENCODE Reference Data:Other genome features
key          = 3-frame translation (forward)
citation     = This track shows the position of stop codons at low magnifications,
	and the 3-frame translation at high magnifications.  Only the forward strand
	is shown.

[DNA/GC Content]
glyph          = dna
global feature = 1
strand         = both
gc_window      = auto
height         = 40
fgcolor        = red
key            = DNA/GC Content
category       = non-modENCODE Reference Data:Other genome features

[TranslationR]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = blue
strand       = -1
start_codons = 0
arrow_height = 2
translation  = 3frame
category     = non-modENCODE Reference Data:Other genome features
key          = 3-frame translation (reverse)
citation     = This track shows the position of stop codons at low magnifications,
	and the 3-frame translation at high magnifications.  Only the reverse
	strand is shown.


#[OSTB]
#feature       = expressed_sequence_match:BLAT_OST_BEST
#glyph         = segments
#category      = non-modENCODE Reference Data: mRNAs from WormBase
#draw_target   = 1
#show_mismatch = 1
#ragged_start  = 1
#height        = 5
#bgcolor       = black
#fgcolor       = black
#connector     = solid
#group_pattern = /^Sequence:OST[RF]/
#link          = sub {
#                        my $feature = shift;
#                        my $name = $feature->name;
#                        $name =~ s/^Sequence:OST[FR](10|30)/$1/;
#                        $name =~ s/^Sequence:OST[FR]/10/;
#                        $name =~ s/_\d*//;
#                        $name =~ s/([A-Z]+\d+)$/\@$1/;
#                        return qq[http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?by=plate&sid=$name];
#                        }
#label       = sub{my $name = shift->id;
#                  $name =~ s/Sequence:(.+)_\d$/$1/;
#	          return $name;}
#link_target   = _blank
#key           = ORFeome sequence tags
#citation      = These are <a href="http://worfdb.dfci.harvard.edu/">ORFeome project</a> sequence reads.
#        The ORFeome project designs primer assays for spliced mRNAs and then performs sequence reads
#        on rtPCR material, producing "OSTs."  This track shows ORFeome project OSTs aligned to the
#        <i>C. japonica</i> genome using Jim Kent's BLAT program
#        [<a href="http://genome.cse.ucsc.edu/cgi-bin/hgBlat">http://genome.cse.ucsc.edu/cgi-bin/hgBlat</a>].
#        This track shows the best unique location for each OST.  Blue boxes
#        show RST sequences from 5' and 3' RACE experiments using SL1/and SL2 as the 5' universal primer (Kourosh
#        Salehi-Ashtiani, Vidal Lab).

#[OSTB:50000]
#feature   = expressed_sequence_match:BLAT_OST_BEST

#[OSTB:101]
#fontcolor     = black
#height        = 5

[ESTB:100000]
label        = 0
bump         = 0
desciption   = 0

[ESTB:50000]
feature   = EST_match:BLAT_EST_BEST

[ESTB:101]
fontcolor     = black
height        = 5

[ESTB]
feature       = EST_match:BLAT_EST_BEST
glyph         = segments
sort_order    = name
category      = non-modENCODE Reference Data: mRNAs from WormBase
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
height        = 5
bgcolor       = limegreen
fgcolor       = black
label         = sub {my $lab = shift->name;
		     $lab =~ s/Sequence://i;
                     $lab;}
connector     = solid
group_pattern = /\.[35]$/
key           = ESTs (all)
citation      = These are C. japonica expressed sequence tags (ESTs), that have been aligned to
        the C. japonica genome using Jim Kent's BLAT program [<a href="http://genome.cse.ucsc.edu/cgi-bin/hgBlat">
        http://genome.cse.ucsc.edu/cgi-bin/hgBlat</a>].
        This track shows the best unique location for each EST.
        The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line.


[ESTBSPLICED:100000]
label        = 0
bump         = 0
desciption   = 0

[ESTBSPLICED]
feature       = EST_match:BLAT_EST_BEST
glyph         = segments
sort_order    = name
filter        = sub {shift->segments > 1}
category      = non-modENCODE Reference Data: mRNAs from WormBase
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
height        = 5
bgcolor       = limegreen
fgcolor       = black
label         = sub {my $lab = shift->name;
                     $lab =~ s/Sequence://i;
		     $lab;}
connector     = solid
group_pattern = /\.[35]$/
key           = ESTs (spliced)
citation      = The subset of C. japonica expressed sequence tags (ESTs) that span introns, aligned to
        the C. japonica genome using Jim Kent's BLAT program [<a href="http://genome.cse.ucsc.edu/cgi-bin/hgBlat">
        http://genome.cse.ucsc.edu/cgi-bin/hgBlat</a>].
        This track shows the best unique location for each EST.  
        The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line.


[Motifs:region]
feature      = repeat_region:RepeatMasker
glyph        = span
height       = 5
description  = 0
key          = Complex Repeats

[COMPEX_repeats:30001]
description      = 0
label            = 0

[COMPLEX_repeats]
feature          = repeat_region:RepeatMasker
glyph            = generic
height           = 5
bgcolor          = red
fgcolor          = black
bump             = 0
box_subparts     = 2
label            = 1
category         = non-modENCODE Reference Data:Repeats
key              = Complex Repeats
citation         = This track contains matches to long repetitive elements detected using the HMMFS and RepeatMasker programs.

[SIMPLE_repeats:10001]
description      = 0
label            = 0

[SIMPLE_repeats]
feature          = inverted_repeat:inverted
                   tandem_repeat:tandem
glyph            = generic
height           = 5
bgcolor          = yellow
fgcolor          = black
bump             = 0
label            = sub {
                    my $f = shift;
                    my @aliases = $f->each_tag_value('Note');
                    my $coord = $f->ref.":".$f->start."..".$f->stop;
                    return $aliases[0]."; ".$coord;
                   }
description      = sub {
                     return shift->method;
                   }
category         = non-modENCODE Reference Data:Repeats
key              = Simple Repeats
citation         = This track indicates the position of short exact tandem and inverted repetitive elements.

## IMPORTED TRACKS:

##include imported_conf/worm*.conf

## MODENCODE TRACKS:

## HENIKOFF TRACKS:

##include henikoff.ce_conf/*.conf

## LIEB TRACKS:

##include lieb_conf/*.conf

## PIANO TRACKS:

##include piano_conf/*.conf

## SNYDER TRACKS:

##include snyder_conf/*.conf

## WATERSTON TRACKS:

#include waterston_japonica_conf/*.conf