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scproteome.conf
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[GENERAL]
description = Saccharomyces cerevisiae Proteome
database = scproteome
initial landmark = ACT1
# examples to show in the introduction
examples = NOT1 YDR007W Ribosome Vacuolar
units = aa
# zoom levels
zoom levels = 30 60 150 300 600 1200 2400 4800 6000 15000
autocomplete = 1
verbose = 1
show tracks = 1
image cachetime = 120
#plugins
plugins = FastaDumper TrackDumper Submitter BatchDumper ProteinDumper
#aggregators =
# 'region' or 'contig' would be other typical choices,
#reference class = protein - disables nav buttons with current db
default varying = 1 # tracks appear as defined below, not in alphabetical order
# where to link to when user clicks in detailed view
link = "http://www.yeastgenome.org/cgi-bin/locus.pl?locus=$name";
# what image widths to offer
image widths = 640 800 1024 1280
# default width of detailed view (pixels)
default width = 800
default tracks = ORF HMMDomains SignalP TMHMM Profile Vogtle2009
# max and default segment sizes for detailed view
max segment = 1000000
default segment = 500
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
truecolor = 0
# "automatic" classes to try when an unqualified identifier is given
#automatic classes = protein Sequence
#keystyle = between
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =<p><table><tr><th rowspan="2"><font color="black">The HMM Domains are color coded by source: </font></th><th align="left"><font color="darkorange">oranges/yellows = Pfam,</font><font color="red"> reds = SuperFamily,</font><font color="indigo"> purples = Gene3D,</font></th></tr><tr><th align="left"><font color="forestgreen"> greens = Panther,</font><font color="deepskyblue"> blues = TIGRFAM,</font><font color="sienna"> browns = SMART</font></th></tr></table><p>
html5 =
html6 = <script type="text/javascript" src="/javascript/wz_tooltip.js"></script>
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
#include Gbrowse.initcode.conf
#include ../GBrowse.database.local
# Advanced feature:
# Pop up rubberband menus for submitting selected region to search engines...
#include "detail_select_menu.conf"
#include "submitter_plugin.conf"
[TRACK DEFAULTS]
glyph = generic
database = scproteome
height = 8
bgcolor = slateblue
fgcolor = black
fontcolor = black
font2color = blue
label density = 25
bump density = 2000
###################################
# Plugin configuration
###################################
[ORF]
# after updating bioperl we'll need to change feature line
feature = protein:SGD
glyph = processed_transcript
key = ORF
bgcolor = red
description = \&feat_desc
link = http://www.yeastgenome.org/cgi-bin/locus.pl?locus=$name
#[HydropathyPlot]
##feature = protein:SGD
#glyph = protein
#global_feature = 1
#height = 40
#do_kd = 1
#fgcolor = black
##linewidth =
##bgcolor = turquoise
#connector = solid
#connector_color = black
#axis_color = blue
#link = 0
#key = Kyte-Doolittle Hydropathy Plot
#citation = Kyte-Doolittle hydropathy plot
[HMMDomains]
feature = supported_by_domain_match:HMMPanther supported_by_domain_match:Gene3D supported_by_domain_match:superfamily supported_by_domain_match:HMMPfam supported_by_domain_match:HMMSmart supported_by_domain_match:HMMTigr
glyph = segments
font2color = black
bgcolor = sub {
my $f = shift;
my %colorMap = ('supported_by_domain_match:superfamily' => 'reds',
'supported_by_domain_match:hmmpfam' => 'orangeyellows',
'supported_by_domain_match:gene3d' => 'purples',
'supported_by_domain_match:hmmpanther' => 'greens',
'supported_by_domain_match:hmmtigr' => 'blues',
'supported_by_domain_match:hmmsmart' => 'browns');
my $nKeys = scalar(keys %{$main::seenPfam{$f->type}});
my $nCols = scalar(@{$main::colors{$colorMap{lc($f->type)}}});
$main::seenPfam{$f->type}{$f->name} ||= $main::colors{$colorMap{lc($f->type)}}->[$nKeys % $nCols];
# warn join(' : ',($f->type, $f->name, @{$main::colors{$colorMap{lc($f->type)}}}, $main::seenPfam{$f->type}{$f->name})),"\n";
return $main::seenPfam{$f->type}{$f->name};
}
height = 8
title = sub {
my $f = shift;
my $name = $f->name;
my $type = $f->type;
my $score = $f->score;
my ($featType, $source) = split(/:/, $type);
my ($desc) = $f->get_tag_values("Note");
my $interproUrl = 'http://www.ebi.ac.uk/interpro/IEntry';
$desc =~ s/(IPR[0-9]+)::/<a href=$interproUrl?ac=$1>$1<\/a> /;
$desc =~ s/\"\'//g;
my @data;
push @data, { Key => 'Name:' , Value => "$name" };
push @data, { Key => 'Description:' , Value => "$desc" };
push @data, { Key => 'Score/E-value:', Value => "$score" } if ($score && $score ne '0.0');
hover("$source Domain: $name", \@data);
}
expand = 1
description = 1
#label = 1
link = sub {
my $f = shift;
my $method = lc($f->type);
my %urlHash = ( 'supported_by_domain_match:gene3d' => 'http://www.cathdb.info/cathnode/',
'supported_by_domain_match:hmmpanther' => 'http://www.pantherdb.org/panther/family.do?clsAccession=',
'supported_by_domain_match:superfamily' => 'http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=',
'supported_by_domain_match:hmmtigr' => 'http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?user=access&password=access&acc=',
'supported_by_domain_match:hmmsmart'=> 'http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=',
'supported_by_domain_match:tigr' => 'http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=',
'supported_by_domain_match:hmmpfam' => 'http://pfam.sanger.ac.uk/family?type=Family&entry=');
my $urlRoot = $urlHash{$method};
my $lookupId = $f->name;
$lookupId =~ s/(PTHR[0-9]+)_(.+)/$1:$2/;
$lookupId =~ s/^G3DSA_// if ($lookupId =~ /^G3DSA_/);
return "$urlRoot".$lookupId;
}
key = HMM Domains
citation = HMM domains
[SignalP]
feature = supported_by_domain_match:SignalPHMM
glyph = segments
font2color = black
bgcolor = navy
height = 8
label = 0
description = 0
key = Signal Peptide
link = http://www.cbs.dtu.dk/services/SignalP/background/
citation = Signal peptide predictions by SP-HMM/SP-NN
[TMHMM]
feature = supported_by_domain_match:TMHMM
glyph = segments
font2color = black
bgcolor = navy
height = 8
link = http://www.cbs.dtu.dk/services/TMHMM/TMHMM2.0b.guide.php
label = 0
description = 0
key = Transmembrane Domains
citation = Transmembrane domains detected by TmHMM
title = sub {
my $f = shift;
my $ref = $f->seq_id;
my $beg = $f->start;
my $end = $f->end;
my @data;
push @data, { Key => '[', Value => "$ref: $beg\.\.$end\]"};
hover("Transmembrane Domain", \@data);
}
[Profile]
feature = supported_by_domain_match:BlastProDom supported_by_domain_match:ProfileScan
glyph = graded_segments
font2color = black
bgcolor = wheat
title = sub {
my $f = shift;
my $name = $f->name;
$name =~ s/\"\'//g;
my $score = $f->score;
my ($desc) = $f->get_tag_values("Note");
$desc =~ s/\"\'//g;
$desc ||= "<i>unavailable</i>";
$desc =~ s/\001.*//;
my @data;
push @data, { Key => 'Name:', Value => "$name" };
push @data, { Key => 'Description:', Value => "$desc" };
push @data, { Key => 'Score/E-value:', Value => "$score" } if ($score && $score ne '0.0');
hover("Profile Match: $name", \@data);
}
description = 1
label = 0
link = sub {
my $f = shift;
my $urlRoot;
my $lookupId = $f->name;
if ($lookupId =~ /^PD/) {
$urlRoot = 'http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=';
}
if ($lookupId =~ /^PS/) {
$urlRoot = 'http://ca.expasy.org/cgi-bin/prosite-search-ac?';
}
return "$urlRoot".$lookupId;
}
key = Profile Hits
citation = Profile Hits
[Vogtle2009]
feature = mature_protein_region:Vogtle_2009
category = Protein Processing
glyph = segments
font2color = black
bgcolor = blue
title = sub {
my $f = shift;
my $name = $f->name;
$name =~ s/\"\'//g;
my ($dispName) = split("_", $name);
my $start = $f->start;
my $end = $f->end;
my $desc;
($desc) = $f->attributes('presequence') if $f->has_tag('presequence');
$desc =~ s/\"//g;
$desc =~ s/ //g;
my @descArray = split("", $desc);
$desc = join("", @descArray[0..9])."..." if (scalar @descArray > 10);
$desc = 'none' if ($desc eq " " || $desc eq "");
my @data;
push @data, { Key => 'Name:', Value => $name };
push @data, { Key => 'Presequence:', Value => $desc };
hover("Mature Protein Region : [$dispName:$start..$end]", \@data);
}
description = 1
link = /cgi-bin/gbrowse/scproteome/?name=$name
label = 0
key = Experimentally determined mitochondrial protein N termini: Vogtle et al. (2009)
citation = <b>Vogtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, Gevaert K, Kellermann J, Voos W, Sickmann A, Pfanner N, Meisinger C. (2009) Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139(2):428-39. <a href="http://www.ncbi.nlm.nih.gov/pubmed/19837041">[PMID:19837041]</a><br><br>Vogtle et al. performed sequencing of N-terminal peptides derived from highly purified mitochondrial proteins to determine protein N termini. This track represents high-confidence data for 289 proteins, provided by the authors to SGD.</br>