fly.conf

# Main FLY config file

[GENERAL]
description     = D. melanogaster modENCODE (FlyBase R5.32) 
database        = fly
category default state = closed
category tables = 'RNA Expression Profiling: mRNA: RNA-Seq: Developmental Stage' 'MultiMapper UniqueMapper' 'embryo_0-2hr embryo_2-4hr embryo_4-6hr embryo_6-8hr embryo_8-10hr embryo_10-12hr embryo_12-14hr embryo_14-16hr embryo_16-18hr embryo_18-20hr embryo_20-22hr embryo_22-24hr L1 L2 L3+12hr L3_PS1-2 L3_PS3-6 L3_PS7-9 WPP WPP+12hr WPP+24hr WPP+2d WPP+3d WPP+4d Adult_Female+1d Adult_Female+5d Adult_Female+30d Adult_Male+1d Adult_Male+5d Adult_Male+30d'
		  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line (stranded)' 'MultiMapper UniqueMapper' '1182-4H ML-DmBG1-c1 BG2c2 CME_L1 CME_W2 GM2 Kc167 MBN2 ML-DmD11 ML-DmD16-c3 ML-DmD17-c3 ML-DMD20-c5 ML-DmD21 ML-DmD32 ML-DmD4-c1 ML-DmD8 ML-DmD9 S1 S2Rplus S3 Sg4 OSS OSC fGS'
		  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Whole cell' 'CIP-TAP Untreated' 'BG3 Cl.8 Kc167 S2-DRSC S2R+'
 		  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Nuclear' 'CIP-TAP Untreated' 'BG3 Cl.8 Kc167 S2-DRSC S2R+'
		  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Cytoplasmic' 'CIP-TAP Untreated' 'BG3 Cl.8 Kc167 S2-DRSC S2R+'
		  'RNA Expression Profiling: mRNA: RNA-Seq: RNAi depletion of splicing factors (S2 cells)' 'UniqueMapper MultiMapper' 'Control CG10128 CG9373 CG8781 CG8636 CG7437 CG6779 CG6227 CG5655 CG33106 CG32423 CG17838 CG1101 CG10203 CG8749 CG5821 CG5170 CG4602 CG6841 CG6203 CG5422 CG8912 CG8241 CG16901 CG13425 CG10279 CG6049 CG3312 CG31716 CG30122 CG1126 CG8019 CG7971 CG4816 CG3584 CG1646 CG10851 CG5099 CG4760 CG18350 CG16788 CG1559 CG10377 CG9412 CG6946 CG1987 CG9983 CG5442 CG31000 CG17136 B.Control CG4878 CG4262 CG18426 CG12749 CG7878 CG5836 CG3249 CG10328 CG8144 CG12357 CG16725 CG3613 CG42670 CG6987 CG9998 EmptyVector'
                  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Whole cell' 'CIP-TAP Untreated' 'BG3_Whole_cell_CIP-TAP Cl.8_Whole_cell_CIP-TAP Kc167_Whole_cell_CIP-TAP S2-DRSC_Whole_cell_CIP-TAP S2R+_Whole_cell_CIP-TAP'
                  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Nuclear' 'CIP-TAP Untreated' 'BG3_Nuclear_CIP-TAP Cl.8_Nuclear_CIP-TAP Kc167_Nuclear_CIP-TAP  S2-DRSC_Nuclear_CIP-TAP S2R+_Nuclear_CIP-TAP'
                  'RNA Expression Profiling: mRNA: RNA-Seq: Cell Line cap-enriched 5 monoP small RNA: Cytoplasmic' 'CIP-TAP Untreated' 'BG3_Cyto_CIP-TAP Cl.8_Cyto_CIP-TAP Kc167_Cyto_CIP-TAP S2-DRSC_Cyto_CIP-TAP S2R+_Cyto_CIP-TAP'
metadata =
        -description             GBrowse database containing information from FlyBase
				 (www.flybase.org) and modENCODE (www.modencode.org).
        -maintainer              Peter Ruzanov <pruzanov@oicr.on.ca>
        -authority               Ensembl
        -coordinates_version     5
        -coordinates             http://www.dasregistry.org/coordsys/CS_DS245
        -source                  Chromosome
        -testrange               2L:7385068..7387651
        -species                 Drosophila melanogaster
        -taxid                   7227

initial landmark = 2L:123000..180000

default features = Genes 9STATE_S2 EMBRYO_polyA

# examples to show in the introduction
examples = ftz
           sos
	   2L:120000..140000
	   2LHet:98860..298860
	   2RHet:433159..633158
	   3LHet:721028..1721027
	   3RHet:1791377..1841377
	   YHet:103159..203158
	   U:3907234..4107234


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/fgb2/gbrowse/worm">
         <img src="/images/worm_small.png"
              border=0 alt="modENCODE logo worm" />
       </a>
     </td>
     <th valign=middle>
       <span style="font:arial;font-size:18pt"><i>D. melanogaster</i> Genome Browser</span>
     </th>
     <td width="20%"></td>
   </tr>
 </table>

# "automatic" classes to try when an unqualified identifier is given
automatic classes = CDS
pad_left          = 200
truecolor         = 1
autocomplete      = 1
seqid_prefix      = chr
galaxy outgoing   = http://main.g2.bx.psu.edu/tool_runner?tool_id=modENCODEfly

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

[fly:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    fly5_32
                -user   nobody
search options = default +autocomplete


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

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

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

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

[celniker_sj:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    celniker_sj
                -user   nobody
search options  = none


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

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


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


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

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

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


# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = fly
height      = 8
bgcolor     = lightgrey
fgcolor     = black
label density = 100
bump density  = 500
feature_limit = 500
link          = AUTO
discoverable  = 1 
show summary  = 1000000
category visibility = "modENCODE Tracks:RNA Expression Profiling" 1
                      "Gene Structure" 1
                      "Developmental Stages" 0
		      "ESTs and mRNAs" 0


# Ucsc plugin configuration
[UcscPlugin:plugin]
db = dm3
user = viewer
pass = viewer
seq_prefix = chr
split_prefix = chr

[UcscChain:plugin]
default_enable = chainDp3

[UcscNet:plugin]
default_enable = netDroAna2 netDp3

[UcscConservation:plugin]
default_enable = multiz15way
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=multiz15way">Ucsc Website</a>
link           = ftp://hgdownload.cse.ucsc.edu/gbdb/dm3/multiz15way/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:FlyBase
               pseudogene:FlyBase
glyph        = gene
height       = 8
bgcolor      = sub {
                 my $f = shift;
                 return 'white' if $f->primary_tag eq 'pseudogene';
                 return $f->strand < 1 ? 'turquoise' : 'violet';
               }
utr_color    = silver
label        = sub {
                my $f = shift;
                my $dn = $f->display_name;
                my @aliases = $f->each_tag_value('Alias');
                foreach (@aliases) {
                   return "$dn ($_)" if /^\w+-\d+/;
                }
                return $dn;
        }
filter       = sub {
                 my @subf = eval{shift->get_SeqFeatures('mRNA')};
                 return @subf > 0;
              }
description  = sub {
        my $f = shift;
        my @subf = eval{$f->get_SeqFeatures};
        my $note;
        for my $sf (@subf) {
           next unless $sf->primary_tag =~ /RNA|pseudo/;
           $note ||= join '; ',$sf->each_tag_value('Note');
        }
        $note;
  }
link         = http://www.flybase.org/cgi-bin/uniq.html?species=Dmel&field=SYN&db=fbgn&context=$name&caller=quicksearch
label_transcripts =  sub { return shift->primary_tag eq 'mRNA' }
das category = transcription
key          = FlyBase Genes
category     = Annotations for Curated and Predicted Genes from FlyBase
citation     = Annotated gene models from FlyBase Release R5.32 Sep 2010.

[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
citation       = This track show the %GC of the displayed sequence region.  When zoomed in close enough, the DNA sequence is displayed

[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.


[EST:100000]
bump          = 0
label         = 0

[EST:101]
fontcolor     = black
height        = 5

[EST]
feature       = match:sim4_na_dbEST.diff.dmel
glyph         = segments
labels        = 1
label         = sub {
                 my $n = shift->name;
                 $n =~ s/\..+//;
                 $n;
               }
category      = non-modENCODE Reference Data: mRNAs from FlyBase
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
height        = 5
bgcolor       = limegreen
fgcolor       = black
connector     = solid
key           = EST (all)
citation      = EST ("expressed sequence tags") indicated in light green.   <i>D. melanogaster</i> EST sequences submitted to the
                sequence databases prior to 2003 aligned using sim4 (Florea, et al., 1998, Genome Res. 8:967-74) to Release
                3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. D. melanogaster EST sequences submitted since 2003
                aligned to Releases 4 and 5 by NCBI and submitted to FlyBase.

[ESTSPLICED:100000]
bump          = 0
label         = 0

[ESTSPLICED]
feature       = match:sim4_na_dbEST.diff.dmel
glyph         = segments
labels        = 1
label         = sub {
                 my $n = shift->name;
                 $n =~ s/\..+//;
                 $n;
               }
filter        = sub {
                  shift->segments > 1;
               }
category      = non-modENCODE Reference Data: mRNAs from FlyBase
draw_target   = 1
show_mismatch = 1
ragged_start  = 1
height        = 5
bgcolor       = limegreen
fgcolor       = black
connector     = solid
key           = EST (spliced)
das category  = transcription
citation      = EST ("expressed sequence tags") that span an intron are indicated in light green.   <i>D. melanogaster</i> EST sequences submitted to the
                sequence databases prior to 2003 aligned using sim4 (Florea, et al., 1998, Genome Res. 8:967-74) to Release
                3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. D. melanogaster EST sequences submitted since 2003
                aligned to Releases 4 and 5 by NCBI and submitted to FlyBase.


[CONGO:20001]
strand_arrow  = 0
bump          = 0
label         = 0
fgcolor       = yellow

[CONGO]
feature       = match:CONGO
strand_arrow  = 1
bgcolor       = yellow
height        = 6
category      = Annotations for Curated and Predicted Genes from FlyBase
key           = CONGO exons
label density = 100
citation      = Data imported from flybase. Region of sequence conservation across multiple Drosophila species, with a pattern of conservation
                indicative of a protein-coding extent and termini consistent with exon structure (start, splice or stop); submitted by M. Lin and M. Kellis.

[AUGUSTUS:20001]
strand_arrow  = 0
bump          = 0
label         = 0
fgcolor       = green

[AUGUSTUS]
feature       = match:augustus
strand_arrow  = 1
bgcolor       = sub{return shift->strand < 1 ? 'cyan' : 'violet';}
height        = 6
connector     = solid
category      = Annotations for Curated and Predicted Genes from FlyBase
key           = AUGUSTUS
label density = 100
citation      = AUGUSTUS gene predictions from FlyBase.


#[Affy2:10001]
#label         = 0
#bump          = 0
#strand_arrow  = 0

#[Affy2]
#feature       = oligonucleotide:Affymetrix_v2
#category      = Genome Reagents
#strand_arrow  = 1
#height        = 6
#bgcolor       = orange
#fgcolor       = orange
#label density = 100
#bump density  = 100
#key           = Affymetrix Probes (GeneChip for Drosophila Genome 2.0)
#citation      = Data imported from FlyBase. Oligonucleotides (25-mers) designed by Affymetrix to correspond to annotated transcripts in D. melanogaster. Used for the Affymetrix GeneChip Drosophila Genome 2.0 Array, release date July 1, 2004. The GeneChip® Drosophila Genome 2.0 Array provides comprehensive coverage of the Drosophila melanogaster genome and is an important tool for developmental biology. The array canbe used to study expression of over 18,500 Drosophila melanogaster transcripts and was developed based on the content from the recent annotation (release 3.1) of the Drosophila melanogaster genome by FlyBase and the Berkeley Drosophila Genome Project (BDGP), funded by the National Human Genome Research Institute, Department of Energy, and the Howard Hughes Medical Institute. In addition, other published gene predictions from the Drosophila Research community were included on the array.
#label         = 1

[TRANSPOSON]
feature           = transposable_element
glyph             = span
fgcolor           = blue
key               = Natural Transposons
category          = non-modENCODE Reference Data:Other genome features
citation          = From FlyBase: Natural transposons indicated in blue. Extent of a natural transposable element in the sequenced strain (at the time it was sequenced).
                    transposon insertions sites are indicated as red triangles.

[TRANSPOSON_IS]
feature           = transposon_ins_site
glyph             = triangle
orient            = S
fgcolor           = red
bgcolor           = red
point             = 1
height            = 6
key               = Transposon insertion site
citation          = From FlyBase: Mapped transposon insertions sites are indicated as red triangles.
category          = non-modENCODE Reference Data:Other genome features

# Some reservations about putting tRNAs and ncRNAs in a category other than genes
# but the tracks were specifically requested and would otherwise be lost amongst
# coding gene models
[TRNA]
feature          = gene:FlyBase
filter           = sub { shift->name =~ /^tRNA/ }
glyph            = generic
bgcolor          = white
fgcolor          = black
height           = 5
description      = 1
key              = tRNAs
category         = non-modENCODE Reference Data:Non-coding RNAs from FlyBase Genome Features miRBase

[NCRNA]
feature           = gene:FlyBase
filter            = sub {
                    my @subf = eval{shift->get_SeqFeatures};
                    return grep {!/mRNA|tRNA/} @subf;
                  }
glyph            = generic
strand_arrow     = 1
bgcolor          = wheat
fgcolor          = black
height           = 5
description      = 1
key              = Non-coding RNAs
category         = non-modENCODE Reference Data:Non-coding RNAs from FlyBase Genome Features miRBase
citation         = From Flybase: noncoding RNAs, including snRNAs, snoRNA, miRNAs, ncRNAs and rRNAs. Extent of transcribed region corresponding
                   to an annotated non-coding RNA (intron structure not shown)

### IMPORTED TRACKS:

#include imported_conf/fly*.conf

### MODENCODE TRACKS:

## CELNIKER TRACKS

#include celniker_conf/*.conf

## HENIKOFF TRACKS

#include henikoff.dm_conf/*.conf

## KARPEN TRACKS

#include karpen_conf/*.conf

## LAI TRACKS

#include lai_conf/*.conf

## MACALPINE TRACKS

#include macalpine_conf/*conf

## OLIVER TRACKS

#include oliver_conf/*conf

## WHITE TRACKS

#include white_conf/*.conf