[GENERAL]
description = C. elegans (current release)
db_adaptor  = Bio::DB::GFF
db_args     = -dsn dbi:mysql:database=elegans_X;host=localhost
aggregators = clone 
	alignment 
	waba_alignment 
	pseudo{exon:Pseudogene/Pseudogene}
	full_transcript{coding_exon,five_prime_UTR,three_prime_UTR/Transcript}
	RNA{exon/Transcript}
	processed_transcript{coding_exon,five_prime_UTR,three_prime_UTR/CDS}
	coding{coding_exon}
user        = nobody
passwd      = 

# Installed plugins
plugins = Aligner
	  FastaDumper 
          OligoFinder RestrictionAnnotator
	  GFFDumper
	  BatchDumper

# Web site configuration info
stylesheet  = /gbrowse/gbrowse.css
buttons     = /gbrowse/images/buttons
tmpimages   = /gbrowse/tmp

keystyle = between
empty_tracks = key

landmark features = Sequence:Chromosome region:Link

# landmark_padding = 1000

# Default glyph settings
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100

# where to link to when user clicks in detailed view
link          = http://www.wormbase.org/db/get?name=$name;class=$class
link_target   = _new

# what image widths to offer
image widths  = 450 640 800 960 1024 1280

# default width of detailed view (pixels)
default width = 800
default features = CG OP GB LOCI:overview

# max and default segment sizes for detailed view
max segment = 1000000
default segment = 50000

# low-res boundary
low res = 200000

# standard zoom levels to be offered to user
zoom levels    = 100 200 500 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

# fine zoom to be offered -- please provide a percentage
fine zoom      = 20%

# canonical features to show in overview
overview bgcolor = #93CBF4

# routines to compile in advance
init_code = sub ostp_color {
		my $feature = shift;
		my ($amp)  = eval{$feature->attributes('Amplified')};
		return 'grey' unless defined $amp;
		return 'green' if $amp;
		return 'red'   if !$amp;
	}
	sub ostp_amplifies {
		my $feature = shift;
		my ($amp)  = eval{$feature->attributes('Amplified')};
		return '' unless defined $amp;
		return "amplifies"          if $amp;
		return 'does not amplify'   if !$amp;
	}


header = 

footer = <hr>
        <b>Data mirrored from <a href="http://www.wormbase.org">WormBase</b>
	<table width="100%">
	<TR>
	<TD align="LEFT" class="databody">
	For the source code for this browser, see the <a href="http://www.gmod.org">
	Generic Model Organism Database Project.</a>  For other questions, send
	mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
	</TD>
	</TR>
	</table>

# examples to show in the introduction
examples = IV 
           rhodopsin
	   IV:120,000..130,000 
	   unc-9
	   him-*
	   B0019 
	   PCR_product:sjj_B0019.1
           ttattaaacaatttaa
	   
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Transcript Locus Gene GMap PCR_product Operon Genbank Allele

# List of remote annotation sources: format is URL/name pairs separated by
# white space.  Please use quotation marks to prevent internal spaces from
# being interpreted.
remote sources = "Gene Knockout Consortium Alleles" http://aceserver.biotech.ubc.ca/knockout_alleles

[TRACK DEFAULTS]
font2color = blue

# what to show in the overview section
[LOCI:overview]
feature       = gene:landmark
label         = 1
glyph         = generic
bgcolor       = lavender
key           = Landmarks
height        = 5


##################################################################################
# the remainder of the sections configure particular tracks to show
##################################################################################
[CG]
feature      =  
		full_transcript:Coding_transcript
		pseudo:Pseudogene
		miRNA_primary_transcript:miRNA 
		rRNA_primary_transcript:rRNA
		scRNA_primary_transcript:scRNA
		snRNA_primary_transcript:snRNA
		snoRNA_primary_transcript:snoRNA
	        tRNA_primary_transcript:tRNAscan-SE-1.23 
		nc_primary_transcript:Non_coding_transcript
		RNA:RNA
category     = Genes
category:fr  = Gènes
glyph        = processed_transcript
bgcolor      = sub { my $f = shift; return $f->strand > 0 ? 'violet':'turquoise'}
fgcolor      = black
forwardcolor = violet
reversecolor = turquoise
utr_color    = gray
font2color   = blue
label        = sub {
		my $feature = shift;
		my $desc = join ' ',$feature->notes;
		my $name = $feature->display_name;
		return $desc =~ /(\w{3,4}-\d+)$/ ? "$1 ($name)" : $name;
	}
height       = sub {
	my $feature = shift;
	return $feature->method =~  /transcript|UTR|coding_exon/i ? 10 : 6;
	}
description  = sub {
	my $feature = shift;
	my $notes = join ' ',$feature->notes;
	my $source = $feature->source;
	$source =~ s/scan-SE.*$//;  # get rid of SE-1.11 part
	$source =~ s/Coding_transcript/curated coding gene/;
	$notes =~ s/\w{3,4}-\d+$//;   # name is already in label
	if ($source eq 'tRNA') {
               'tRNA'
	} elsif ($feature->method eq 'pseudo') {
		$notes ? " (pseudogene)" : "(pseudogene)";
	} else {
		$notes ? "$notes ($source)" : "($source)";
	}
    }
title        = WormBase gene $name
key          = Gene Models
citation     = 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.  Please select the RNA for more
	details.

[CG:75000]
feature      = Transcript:Coding_transcript Sequence:RNA
glyph        = generic
strand_arrow = 1
bgcolor      = sub {shift->strand>0?'violet':'turquoise'}


[CDS]
feature      = coding:Coding_transcript
glyph        = cds
frame0f      = cadetblue
frame1f      = blue
frame2f      = darkblue
frame0r      = darkred
frame1r      = red
frame2r      = crimson
category     = Genes
description  = 0
require_subparts = 1
height       = 13
label        = sub { my $feature = shift; return "Frame usage for ".$feature->name }
key          = Coding Segments
citation     = This track shows the reading frames of coding segments (also known as "CDS" features).  
	At low magnifications, each transcript

[HISTORICAL]
feature      = processed_transcript:history
glyph        = transcript
bgcolor      = white
description  = sub { 
		my $f = shift;
		my $name = $f->display_name;
		my ($wp)   = $name =~ /wp(\d+)$/;
		return $wp ? "(changed; WormPep WP$wp)" : "(obsolete)";
	}
citation     = This track shows historical gene models that have been superseded.  The 
		suffix indicates which WormPep release the gene model was last present
		in.
category     = Genes
key          = Obsolete gene models

[HISTORICAL:75000]
feature      = CDS:history
bgcolor      = white
glyph        = generic
strand_arrow = 1

[GENEFINDER]
feature      = processed_transcript:genefinder
glyph        = transcript
category     = Genes
bgcolor      = palevioletred
fgcolor      = palevioletred
key          = GeneFinder Predictions

[GENEFINDER:75000]
feature      = CDS:genefinder
key          = GeneFinder Predictions

[OP]
feature      = operon:operon
glyph        = generic
category     = Genes
strand_arrow = 1
bgcolor      = green
height       = 10
description  = 1
key          = Operons
citation     = These are operons published by Blumenthal et al, Nature 417: 851-854 (2002).

[TS]
feature      = SL1_acceptor_site SL2_acceptor_site
category     = Genes
glyph        = sub {
		my $feature = shift;
		return $feature->source eq 'SL1' ? 'diamond' : 'triangle';
	}
point        = 1
bgcolor      = sub {
	    my $feature = shift;
            return $feature->source eq 'SL1' ? 'red' : 'green';
	}
font2color   = 'red';
height       = 8
label        = 0
label density = 100
description  = sub {
		shift->source;
	}
key          = Trans-splice acceptor
citation     = These are SL1 and SL2 trans-splice acceptors published by Blumenthal et al, Nature 417: 851-854 (2002).

# This track shows the approximate physical span of genetic intervals
[GENETIC]
feature       = gmap_span:interpolated_pmap_position
		gmap_span:absolute_pmap_position
key           = Genetic limits (experimental)
category     = Genes
glyph         = sub {
                    my $f = shift;
                    return ($f->source eq 'interpolated_pmap_position') ? 'span' : 'box';
       }
fgcolor       = black
bgcolor       = sub { my $feature = shift;
		      return ($feature->source eq 'interpolated_pmap_position') ? 'red' : 'turquoise';
	}
link          = sub { my $f   = shift;
                      my $name = $f->name;
   	              return "http://www.wormbase.org/db/get?name=$name;class=Gene";
	}
height        = 3
label         = sub { return shift->name; }
description = sub { my $feature = shift;
	              my $notes = join(' ',$feature->notes);
	              $notes =~ /^\s*(\-?\d{1,2}\.\d*)\s(.*)/;
		      # Reduce sig figs to three
	              my $pos  = $1;
		      my $rest = $2;
     	              $rest =~ s/uncloned|cloned//;  # Remove the status descriptor	
		      $pos  = sprintf("%2.3f",$pos);
		      my $formatted = "$pos $rest";
		      return $formatted;
        }
citation      = This experimental track shows the maximal extents for genetic loci.  
		Loci that have been interpolated onto the physical
                map (and whose precise location is unknown) are shown 
                as a thin black span.  The physical extent of such loci are determined 
                by interpolating their genetic position onto the physical 
                map using 95% confidence limits.  Please note that the actual 
                location of such loci may lay outside of the span depicted.
                Loci with known sequence connections are shown in turquoise 
                and depicted using the physical span of the gene.

[WABA]
feature       = waba_alignment
bgcolor       = blue
glyph         = heterogeneous_segments
draw_target   = 1
show_mismatch = 1
realign       = 0
category     = Sequence Similarity Tracks
waba_weak_color   = #A0A0A0
waba_strong_color = cornflowerblue
waba_coding_color = blue
fgcolor       = black
height        = 6
connector     = dashed
box_subparts  = 0
key           = Briggsae alignments
label = sub {	my $feature = shift;
		my $ref   = $feature->target;
		my $start = $feature->target->start;
		my $stop  = $feature->target->end;
	        my $first = ($feature->segments)[0];
                my $strand = defined $first && $first->start>$first->end ? -1 : +1;
		($start,$stop) = ($stop,$start) if $strand < 0;
	        "$ref:$start..$stop";
	}
citation      = These are segments of the C. briggsae rough draft sequence that have been
	aligned to the C. elegans genome using Jim Kent's WABA program [Kent & Zahler, 
	Genome Res 10:1115-25 (2000)].
	WABA distinguishes between low similarity regions (light blue), high-similarity regions
	(medium blue), and regions of high similarity that have the characteristic wobble-base
	mismatch of coding regions (dark blue).  Also see "Briggsae Alignments (BLAST)".
	IMPORTANT NOTE:  Briggsae sequence is available from the GSC BLAST server at 
	<a href="http://genome.wustl.edu/gsc/Blast/client.pl">http://genome.wustl.edu/gsc/Blast/client.pl</a> and the Sanger BLAST server
	at <a href="http://www.sanger.ac.uk/Projects/C_briggsae/blast_server.shtml">http://www.sanger.ac.uk/Projects/C_briggsae/blast_server.shtml</a>.
link = 	sub {
		my $feature = shift;
		my $ref   = $feature->target;
		my $start = $feature->target->start;
		my $stop  = $feature->target->end;
	        my $first = ($feature->segments)[0];
                my $strand = defined $first && $first->start>$first->end ? -1 : +1;
		($start,$stop) = ($stop,$start) if $strand < 0;
		return "http://www.wormbase.org/db/seq/ebsyn?name=$ref:$start..$stop";
	}

[WABA:100000]
feature       = nucleotide_match:waba_weak nucleotide_match:waba_strong nucleotide_match:waba_coding
glyph         = generic
bgcolor       = #E0E0E0

[ESTB:50000]
feature   = EST_match:BLAT_EST_BEST
[ESTB:101]
fontcolor     = black
height        = 5

[ESTB]
feature       = alignment:BLAT_EST_BEST
glyph         = segments
category     = Sequence Similarity Tracks
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
bgcolor       = limegreen
fgcolor       = black
connector     = solid
group_pattern = /\.[35]$/
key           = ESTs aligned by BLAT (best)
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.  Other EST matches, some
	of which may represent repetitive elements, are	shown in the track labeled
	"ESTs aligned by BLAT (other)".
	The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line.

[ESTO]
feature       = alignment:BLAT_EST_OTHER
glyph         = segments
category     = Sequence Similarity Tracks
draw_target   = 1
show_mismach  = 1
ragged_start  = 1
bgcolor       = lightgray
fgcolor       = black
height        = 6
connector     = solid
group_pattern = /\.[35]$/
key           = ESTs aligned by BLAT (other)
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 ESTs that align multiple times, some of which represent repetitive
	regions.  For the "best" match, see the track labeled "ESTs aligned with BLAT (best)".
	The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line.

[ESTO:50000]
feature      = EST_match:BLAT_EST_OTHER

[mRNAB]
feature       = alignment:BLAT_mRNA_BEST alignment:BLAT_ncRNA_BEST
glyph         = segments
category     = Sequence Similarity Tracks
label         = sub {
                my $f = shift;
		my $label = ($f->source =~ /BLAT_mRNA_BEST/) ? 'mRNA' : 'ncRNA';        
	        my $name = $f->name;
		return "$label: $name";
	}
draw_target   = 0
show_mismach  = 1
ragged_start  = 1
bgcolor       = sub {
                my $f = shift;
		return 'yellow' if ($f->source =~ /BLAT_mRNA_BEST/);
		return 'grey';
               }
fgcolor       = black
height        = 6
connector     = solid
key           = RNAs aligned by BLAT (best)
citation      = These are C. elegans full length cDNAs and ncRNAs 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 cDNA.  Other cDNA matches, some
	of which may represent repetitive elements, are	shown in the track labeled
	"RNAs aligned by BLAT (other)".

[mRNAO]
feature       = alignment:BLAT_mRNA_OTHER alignment:BLAT_ncRNA_OTHER
glyph         = segments
category     = Sequence Similarity Tracks
label         = sub {
                my $f = shift;
		my $label = ($f->source =~ /BLAT_mRNA_OTHER/) ? 'mRNA' : 'ncRNA';        
	        my $name = $f->name;
		return "$label: $name";
	}
draw_target   = 1
show_mismach  = 1
ragged_start  = 1
bgcolor       = sub {
                my $f = shift;
		return 'green' if ($f->source =~ /BLAT_mRNA_OTHER/);
		return 'grey';
               }
fgcolor       = black
height        = 5
connector     = solid
key           = RNAs aligned by BLAT (other)
citation      = These are C. elegans full length cDNAs, 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 non-unique matches, which may represent repetitive sequences.
	For the best single alignment, see the track labeled
	"RNAs aligned by BLAT (best)".

[NEMATODE]
feature       = alignment:BLAT_NEMATODE
glyph         = segments
category     = Sequence Similarity Tracks
bgcolor       = lightblue
fgcolor       = black
height        = 4
connector     = solid
key           = Non-elegans ESTs
citation      = These are non-C. elegans nematode ESTs that have been aligned to
	the C. elegans genome using Jim Kent's BLATX program [<a href="http://genome.cse.ucsc.edu/cgi-bin/hgBlat">http://genome.cse.ucsc.edu/cgi-bin/hgBlat</a>].

[NEMATODE:50000]
feature   = translated_nucleotide_match:BLAT_NEMATODE


[RNAi]
feature       = RNAi_reagent:RNAi experimental:RNAi_injection RNAi
category      = Phenotype/Expression Tracks
bgcolor       = goldenrod
fgcolor       = black
height        = 4
key           = RNAi experiments
citation      = This track indicates the location of RNA interference (RNAi) experiments
	that have been performed by a number of groups.  Click on the RNAi element to get
	more information about the experiment.

[SAGE]
feature       = transcript:SAGE_transcript
bgcolor       = silver
category      = Phenotype/Expression Tracks
height        = 5
key           = SAGE probes
link          = sub {
		my $feature = shift;
		my $name    = $feature->name;
	        $name =~ s/^\w+:/SAGE:/;
		"http://www.wormbase.org/db/get?name=$name;class=SAGE_tag"
	}
citation      = This track indicates the location of Serial Analysis of Gene Expression (SAGE)
	probes.  Clicking on this link will take you to a page that summarizes the expression
	patterns associated with these probes.

[EXPR]
feature       = experimental_result_region:Expr_profile
category      = Phenotype/Expression Tracks
bgcolor       = orange
fgcolor       = black
height        = 4
key           = Expression chip profiles
citation      = This track indicates the location of PCR products that have been placed on
	expression chips produced by the C. elegans Microarray Consortium [
	<a href="http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html">http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html</a>]. 
	The genes corresponding to these products have been clustered by their
	expression patterns.  Click on the profile to get more information about the expression
	profile of its corresponding gene.

[Allele]
feature      = sequence_variant:Allele
	       Allele:Allele deletion:Allele substitution:Allele SNP:Allele 
	       insertion:Allele
	       transposable_element_insertion_site:Allele
               transposable_element_insertion_site:Mos_insertion_allele
	       Complex_change_in_nucleotide_sequence:Allele
category      = Variation Tracks
glyph        = sub {
		my $f = shift;
		return 'triangle' if $f->method eq 'Mos_insertion_allele';
		return 'triangle' if $f->method eq 'transposable_element_insertion_site';
		return 'box'  if $f->method =~ /complex_change/i;
		return 'diamond'  if $f->length <= 3 or $f->method eq 'SNP'; # some SNPs come out length 3 -- dunno why
		return 'generic';
	}
bgcolor      = sub {
		my $f = shift;
		my $s = $f->method;
		return 'yellow' if $f->source eq 'Mos_insertion_allele';
		return 'red'    if $s eq 'deletion';
		return 'yellow' if $s eq 'substitution';
		return 'blue'   if $s eq 'transposable_element_insertion_site';
		return 'blue'   if $s =~ /complex_change/i;
		return 'blue'   if $f->length <= 3 or $f->method eq 'SNP';
		return 'white';
	}
fgcolor      = black
font2color   = blue
height       = 8
description  = sub {
		my $f = shift;
		my $s = $f->method;
		return 'Mos insertion' if $f->source eq 'Mos_insertion_allele';
		return 'deletion'      if $s eq 'deletion';
		return 'transposon insertion' if $s eq 'transposable_element_insertion_site';
		return 'insertion'          if $s eq 'insertion';
		return 'insertion/deletion' if $s =~ /complex_change/i;
	        return 'allele'             if $f->length <= 3 and $f->method ne 'SNP';
		if ($f->length <= 3 or $f->method eq 'SNP') {
		    # Fudge factor.  Let's call the SNP verified if it has an allele-like designation
		    return 'SNP (verified)' unless ($f->name =~ /^snp_/);
		    return 'SNP (predicted)';
		}	
 	}
key          = SNPs, Knockouts & Other Alleles
citation      = This track shows alleles and SNPs.  Red boxes are 
	<a href="http://elegans.bcgsc.bc.ca/knockout.shtml">Knockout Consortium</a>
	deletion alleles.  Triangles are transposon insertions engineered by Laurent Segalat and
	others [<a href="http://www.wormbase.org/db/misc/paper?name=%5Bwm99ab757%5D;class=Paper">Alvarez et al.,
	Towards a genome-wide collection of transposon insertions,International C. elegans Meeting 1999 #757</a>].
	Yellow triangles are Mos derived transposon insertions; blue triangles are Tc* derived transposon insertions.
	White boxes represent other types of alleles.

[PCR]
feature       = PCR_product
bgcolor       = violet
glyph         = primers
category      = Reagents
fgcolor       = black
connect       = 1
connect_color = cyan
key           = PCR Assays
citation      = This track indicates the location of primer pairs that have been created by a number
	of groups.  Click on the element to obtain the left and right oligo sequences, information
	about the amplification information, and ordering information (if available).

[PolyA]
feature      = polyA_signal_sequence polyA_site
glyph        = sub {
		my $f = shift;
		return 'diamond' if $f->method =~ /signal/;
		return 'triangle';
	}
category     = Genes
point        = 1
orient       = N
bgcolor      = violet
description  = sub { my $s = shift->source; $s=~tr/_/ /; $s; }
key          = polyA sites and signal sequences
citation     = High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs.


[SeqFeature]
feature      = misc_feature:binding_site
glyph        = sub {
		my $f = shift;
		return 'diamond' if $f->method =~ /signal/;
		return 'triangle';
	}
category      = Misc
#point        = 1
#orient       = N
bgcolor      = green
key          = Binding sites
label        = sub {
		my $f = shift;
		my $source = $f->source;
		my $name = $_->name;
		return "$name (DNA binding site)" if $source eq 'binding_site';
		return $name;
		}     
citation     = 
	This track indicates the position of manually curated binding
	sites extracted from published data. This dataset contains
	experimentally confirmed binding sites as well as
	computationally derived potential bind targets.  Data can be
	verified through the paper evidence attached to each object.

[OSTP]
feature       = PCR_product:Orfeome
glyph         = primers	
category      = Reagents
height        = 4
fgcolor       = black
connect       = 1
connect_color = \&ostp_color
font2color    = \&ostp_color
fgcolor       = \&ostp_color
description   = \&ostp_amplifies
key           = ORFeome Project Primers
citation      = This track contains Orfeome Project primer pairs.  These primers were used to amplify
	C. elegans cDNAs.  A positive amplification, shown in green, is evidence that the region
	between the two primers is transcribed.  Failure to amplify, shown in red, suggests
	either that the gene model is incorrect, or that the gene is expressed at very low levels.
	Detailed gene models derived from ORFeome sequencing will be added to this display in
	the future.  See <i>Reboul et al. Nat. Genet. 2003 Apr 7.</i> and 
	<a href="http://worfdb.dfci.harvard.edu" target="_blank">WORFdb</a> for further information.

[OLIGO]
feature       = reagent:Oligo_set
glyph         = primers
category      = Reagents
height        = 4
fgcolor       = black
connect       = 1
connect_color = black
font2color    = black
fgcolor       = black
key           = Microarray oligo probes
citation      = This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.

[OST]
feature       = expressed_sequence_match:BLAT_OST_BEST
glyph         = segments
category      = Genes
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
bgcolor       = red
fgcolor       = black
connector     = solid
group_pattern = /^OST[RF]/
link          = http://worfdb.dfci.harvard.edu/search.pl?form=1;search=$name
link_target   = _blank
key           = ORFeome sequence tags (best)
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.

[GB]
feature       = region:Genbank
glyph         = arrow
category      = Misc
tick          = +2
base          = 1
relative_coords = 1
key           = Genbank entry
link          = http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=$name[accn]
# link          = ../gbrowse_moby?id=$name;source=$class
citation      = The C. elegans genome was submitted to the GenBank and EMBL databases in
	in the form of a set of minimally-overlapping segments.  This track shows the
	position of these accessioned entries.


[BLASTX]
feature       = protein_match:wublastx
glyph	      = segments
bgcolor       = sub { $_[0]->name =~ /^BP:/ ? 'blue' : 'orange' }
fgcolor       = black
category      = Sequence Similarity Tracks
height        = 4
key           = BLASTX Hits
link          = sub {
  		  my $feature = shift;
	          my $name = $feature->name;
		  if ($name =~ s/^TR://) {
	             return sprintf("http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:%s]+-vn+2",$name);
		  } elsif ($name =~ s/^SW://) {
	             return sprintf("http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-id+3LIc21HeBHW+-e+[SWALL:'%s']",$name);
                  } elsif ($name =~ s/ENSEMBL://) {
                     return sprintf('http://www.ensembl.org/Homo_sapiens/protview?peptide=%s',$name);
                  } elsif ($name =~ s/GADFLY://) {
                     return sprintf('http://hedgehog.lbl.gov:8002/cgi-bin/annot/query?namesearch=%s',$name);
                  } elsif ($name =~ s/SGD://) {
                     return sprintf('http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=%s',$name);
                  } elsif ($name =~ s/PS://) {
                     return sprintf('http://www.expasy.ch/cgi-bin/prosite-search-de?%s',$name);
	          } else {
                     return "http://www.wormbase.org/db/get?name=$name;class=Protein";
	          }
                }
citation =  These are WUBLASTX (nucleotide to protein, via six-frame
	translation) similarity hits, run biweekly against reference protein
	datasets from the genomes of yeast, fly, worm, and human and also
	against a reduced subset of SwissProt and TREMBL.  Blue-colored hits
	indicate similarity hits against C. briggsae predicted proteins.

[EMBL_BEST]
feature       = alignment:BLAT_EMBL_BEST
glyph	      = segments
category      = Sequence Similarity Tracks
bgcolor       = red
fgcolor       = black
height        = 6
key           = BLAT EMBL/GenBank Hits (Best)
link          = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=p&form=1&field=Sequence+ID&term=$name
citation = These are BLAST (nucleotide to nucleotide) similarity hits, run  biweekly
	on the contents of EMBL and GenBank.  This track records the highest-scoring
	matches.

[EMBL_OTHER]
feature       = alignment:BLAT_EMBL_BEST
glyph	      = segments
category      = Sequence Similarity Tracks
bgcolor       = pink
fgcolor       = black
height        = 6
key           = BLAT EMBL/GenBank Hits (Other)
link          = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=p&form=1&field=Sequence+ID&term=$name
citation = These are BLAST (nucleotide to nucleotide) similarity hits, run  biweekly
	on the contents of EMBL and GenBank.  This track records the non-highest scoring
	matches.

[HMM]
feature       = similarity:hmmfs.3 repeat_region:RepeatMasker
category      = Sequence Similarity Tracks
bgcolor       = red
fgcolor       = black
height        = 4
connector     = none
key           = Complex Repeats
citation      = This track contains matches to long repetitive elements detected using the HMMFS and RepeatMasker programs.

[REP]
feature       = tandem_repeat inverted_repeat
bgcolor       = bisque
fgcolor       = black
category      = Misc
height        = 4
key           = Simple Repeats
connector     = none
citation      = This track indicates the position of short exact tandem and inverted repetitive elements.

[CLO]
feature       = clone
fgcolor       = sub {
		my $feature = shift;
		return 'aqua' if !defined $feature->start || !defined $feature->stop;
		return 'black';
	}
category      = Reagents
glyph         = anchored_arrow
height        = 7
key           = YACs & Cosmids
font2color    = aqua
description   = sub {
		my $feature = shift;
		return 'Warning: Clone end(s) not known/shown.'
			unless defined $feature->start && defined $feature->end;
		1;
	}
citation      = This track shows the locations of the cosmids and YACs used for the
	physical mapping and sequencing of the C. elegans genome.  The clone termini
	do not necessarily correspond to the termini of submitted GenBank/EMBL entries.
	In some cases the exact termini of the clones is not known.  For example, YACs
	were sequenced using PCR amplification across gaps in the cosmid maps.  When
	a clone end is not known, it is shown as an arrow extending to the end of the 
	display.  Such data is to be treated with caution.

[LINK]
feature       = region:Link Sequence:Chromosome
fgcolor       = black
glyph         = arrow
category      = Misc
height        = 7
tick          = 2
relative_coords = 1
key           = Links and Superlinks
citation      = This track shows the location and coordinates of contigs
	created during the assembly of the C. elegans genome.

[CANONICAL]
feature       = region:Genomic_canonical
fgcolor       = black
glyph         = arrow
category      = Misc
height        = 7
tick          = 2
relative_coords = 1
key           = Contig submissions
citation      = This track shows the location and coordinates of contigs
	(mostly cosmids) submitted to GenBank/EMBL.

[TranslationF]
glyph        = translation
global feature = 1
frame0       = cadetblue
frame1       = blue
frame2       = darkblue
height       = 20
fgcolor      = purple
start_codons = 0
strand       = +1
arrow_height = 2
translation  = 3frame
category     = DNA
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
height         = 40
fgcolor        = red
category     = DNA

[TranslationR]
glyph        = translation
global feature = 1
frame0       = darkred
frame1       = red
frame2       = crimson
height       = 20
fgcolor      = blue
strand       = -1
start_codons = 0
arrow_height = 2
translation  = 3frame
category     = DNA
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.

[Aligner:plugin]
alignable_tracks   = ESTB ESTO mRNAB WABA
upcase_tracks      = CDS tRNA NG
align_default      = ESTB
upcase_default     = CDS
ragged_default     = 10

[OligoFinder:plugin]
search_segments = I II III IV V X

