worm.conf

# WORM main config

[GENERAL]
description     = C. elegans modENCODE (WormBase build WS220)
database        = worm
category default state = closed
category default state = closed
category state  = "Gene Structure" open
                  "Chromatin Structure" open
                  "RNA Expression Profiling" open
                   Analysis open
category tables = 'Gene Structure:Gene Models:Confirmed Sites' 'Introns PolyA SpliceLeaders' 'N2.4cell.Embryo  N2.EarlyEmbryo.Rep.2  N2.EarlyEmbryo.ArrayCaptured  N2.EarlyEmbryo.0min  N2.EarlyEmbryo.30min  N2.EarlyEmbryo.60min  N2.EarlyEmbryo.90min  N2.EarlyEmbryo.120min  N2.EarlyEmbryo.150min  N2.EarlyEmbryo.180min  N2.EarlyEmbryo.210min  N2.EarlyEmbryo.240min  N2.EarlyEmbryo.270min  N2.EarlyEmbryo.300min  N2.EarlyEmbryo.330min  N2.EarlyEmbryo.360min  N2.EarlyEmbryo.420min  N2.EarlyEmbryo.450min  N2.EarlyEmbryo.480min  N2.EarlyEmbryo.510min  N2.EarlyEmbryo.540min  N2.EarlyEmbryo.570min  N2.EarlyEmbryo.600min  N2.EarlyEmbryo.630min  N2.EarlyEmbryo.660min  N2.EarlyEmbryo.690min  N2.EarlyEmbryo.720min  N2.LateEmbryo.Rep.1  N2.L1.Rep.1  N2.L1.Comb.Reps  N2.L2.Rep.1  N2.L2.Comb.Reps  DauerEntry.Rep.1  DauerEntry.Rep.3  DauerEntry.Rep.4  DauerExit.Rep.1  DauerExit.Rep.2  DauerExit.Rep.3  DauerExit.Rep.4  N2.L3.Rep.1  N2.L3 Comb.Reps  N2.L4.Rep.1  N2.L4.Rep.2  N2.E.faecalis.24hour  fer-15.L4.H.sphaerosporum  fer-15.L4.H.sphaerosporum.control  fer-15.Adult.D.coniospora.5hour  fer-15.Adult.D.coniospora.12hour  fer-15.Adult.Harposporium  fer-15.Adult.Harposporium.control  him-8.Embryo.Male.Rep.1  him-8.Embryo.Male.Rep.2  him-8.Embryo.Male.Comb.Reps  him-8.L4.Male.Rep.1  him-8.L4.Male.Rep.2  him-8.L4.Male.Comb.Reps  JK1107.L4.Rep.1  JK1107.L4.Rep.2  JK1107.L4.Comb.Reps  lin-35.L1  lin-35.L1.ArrayCaptured'

initial landmark = I:143000..180000

default features = Genes LIEB_WIG_CHIPSEQ_TF early_embryo.alignments.ws220.bam.sorted YA_Young_Adult_25dC_46hrs_post-L1.alignments.ws220.bam.sorted

# examples to show in the introduction
examples = I:110643..112642
           V:625000..675000
	   X:120000..140000
	   lin-12

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. elegans</i> Genome Browser</span>
      </th>
      <td width="20%"></td>
    </tr>
  </table>

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Transcript Locus Gene GMap PCR_product 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
#################################

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

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

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

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

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

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

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

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

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

# Default glyph settings
[TRACK DEFAULTS]
glyph         = generic
database      = worm
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      = gene:Coding_transcript
               Pseudogene
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 $name = shift->name;
                   return qq[http://www.wormbase.org/db/get?name=$name;class=Gene];}
label_transcripts =  1
das category = transcription
key          = Curated WormBase WS220 Genes
sort_order   = name
citation     = WS220<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           = gene:snRNA gene:miRNA gene:snoRNA gene:rRNA gene:Non_coding_transcript
database          = worm
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. elegans</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. elegans expressed sequence tags (ESTs), that have been aligned to
        the C. elegans 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. elegans expressed sequence tags (ESTs) that span introns, aligned to
        the C. elegans 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.


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

[HOTREGIONS]
feature      = HR:binding_site
glyph        = heat_map
category     = Transcription Factors: HOT
start_color  = lightblue
end_color    = blue
max_score    = 23
min_score    = 15
fgcolor      = black
height       = 8
label        = sub {
                my $f = shift;
                my $lab = "HOT region: ".$f->score." TFs";
                return $lab;
               }
vary_fg      = 1
balloon hover= sub {
		my $f = shift;
                my $lab = "HOT region: ".$f->score." TFs";
                return $lab;
               }
key          = High Occupancy Target regions
citation     = High Occupancy Target (HOT) regions are defined as genomic regions to which 15 or more independent transcription factors bind.
               This track gives the positions of HOT regions as determined by the S. Kim group.

## 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_conf/*.conf