Difference between revisions of "GBrowse"

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 +
{{SessionHead}}
 +
{| class="tutorialheader"
 +
| {{TutorialTitleLine|GBrowse}}<br />
 +
[[2011 GMOD Spring Training]]<br />
 +
8-12 March 2011<br />
 +
[[User:Scott|Scott Cain]]
 +
| align="right" | {{#icon: GBrowseLogo.png|GBrowse|200|gmod:GBrowse}}
 +
|}
  
  
[[File:GBrowseLogo.png|center|400px|alt=GBrowse logo]]
+
{{TocRight}}
 +
=Prerequisites=
  
<div class="componentBox">
+
Installed before using apt or cpan.
<div class="compBoxHdr">Status</div>
+
*Mature release
+
*maintenance
+
*active support
+
<div class="compBoxHdr">Resources</div>
+
*[http://gbrowse.org Home page]
+
*[http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ Download]
+
*[http://gmod.org/extras/2008GMODCommunitySurvey.html#GBrowse 2008 Survey]
+
*[[GBrowse Tutorial]]
+
</div>
+
  
==About Generic Genome Browser (GBrowse)==
+
=Install GBrowse=
  
GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
+
Easily installed via the cpan shell:
 +
  <span class="enter">sudo cpan</span>
 +
  cpan> <span class="enter">install Bio::Graphics::Browser2</span>
  
* Simultaneous bird's eye and detailed views of the genome.
+
Which gets all of the prereqs that aren't installed on the machine.
* Scroll, zoom, center.
+
* Use a variety of [[GBrowse Configuration HOWTO#Glyphs and Glyph Options|premade glyphs]] or create your own.
+
* Attach arbitrary URLs to any annotation.
+
* Order and appearance of tracks are customizable by administrator and end-user.
+
* Search by annotation ID, name, or comment.
+
* Supports third party annotation using [[GFF]] formats.
+
* Settings persist across sessions.
+
* DNA and [[GFF]] dumps.
+
* Connectivity to different databases, including [[BioSQL]] and [[Chado]].
+
* Multi-language support.
+
* Third-party feature loading.
+
* Customizable [[GBrowse Plugins|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|design primers]], create restriction maps, edit features)
+
  
Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.
+
=Tutorial=
Visit the [http://gbrowse.org GBrowse website].
+
  
===Screenshots===
+
Go to http://localhost/gbrowse2
  
[[image:GBrowse_screenshot1.png|none|thumb|350px|GBrowse running on [http://hapmap.ncbi.nlm.nih.gov/downloads/index.html HapMap.org] [[Media:GBrowse_screenshot1.png|Click to view at full resolution]]]]
+
=Basic [[Chado]] Configuration (if we have time)=
  
==Downloads==
+
{{CPAN|Bio::DB::Das::Chado}} was installed when we created the image.  Sample configuration files are available with GBrowse, and we'll get the sample Chado file:
  
Download GBrowse: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/]
+
  <span class="enter">wget http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/contrib/conf_files/07.chado.conf -O pythium.conf</span>
  
The development version of GBrowse is found at https://github.com/GMOD/GBrowse. Please be aware that development versions may have new features that are not fully tested.
 
  
Note that GBrowse can also be found on [http://search.cpan.org CPAN] and in the Debian sid ("unstable") apt package repository (so it is available to install via apt-get in Ubuntu since release 12.04).
 
  
==Using GBrowse==
+
Some simple tweaks and additions:
  
===System Requirements===
+
*Change description
 +
*Get rid of <tt>database = main</tt>
 +
*Remove or change examples (yeast examples don't help anybody)
 +
*Add initial landmark (<tt>initial landmark = scf1117875582023</tt>)
  
GBrowse is [[Glossary#Perl|Perl]]-based and the GBrowse 2.x modules are [http://search.cpan.org/dist/GBrowse/ hosted on CPAN]. GBrowse can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed.
+
==DB connection info==
  
===Installation===
+
[annotation:database]
 +
db_adaptor    = Bio::DB::Das::Chado
 +
db_args      = -dsn dbi:Pg:dbname=chado
 +
                -user gmod
 +
                -inferCDS 1
 +
                -srcfeatureslice 1
 +
search options = default
  
* [[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]
+
==Add a BAM data source==
* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]
+
* [[GBrowse 2.0 Install Paths|Install Paths]]
+
  
===Configuration===
+
[bam_sample:database]
 +
db_adaptor    = Bio::DB::Sam
 +
db_args        = -fasta /var/www/gbrowse2/databases/pythium/scf1117875582023.fasta
 +
                  -bam  /var/www/gbrowse2/databases/pythium/simulated-sorted.bam
 +
search options = default
  
* [[GBrowse 2.0 Configuration HOWTO|Configuration guide]]
+
==Add track defaults==
** [[GBrowse Configuration/Authentication|Authentication]]
+
** [[GBrowse Configuration/Balloons|Balloons]]
+
** [[GBrowse Configuration/DAS|DAS]]
+
** [[GBrowse Configuration/Feature frequency histograms|Feature Frequency Histograms]]
+
** [[GBrowse Configuration/Glyphs|Glyphs]]
+
** [[GBrowse Configuration/I18n|I18n]]
+
** [[GBrowse Configuration/Images|Images]]
+
** [[GBrowse Configuration/URL schema|URL schema]]
+
* [[Creating and Managing Subtracks with GBrowse2|Subtracks]]
+
* [[GBrowse Adaptors]]
+
* [[GBrowse Backends]]
+
  
===Documentation===
+
[TRACK DEFAULTS]
 +
glyph      = generic
 +
database    = annotation
 +
height      = 8
 +
bgcolor    = cyan
 +
fgcolor    = black
 +
label density = 25
 +
bump density  = 100
  
* [[GBrowse FAQ]]
+
Note particularly the "database" entry--for most tracks we'll be using the annotation database, but the bam_sample data source will be available when we want it.
* [http://search.cpan.org/dist/GBrowse/htdocs/annotation_help.html Annotation Help]
+
* Balloons:
+
** [[GBrowse Popup Balloons]]
+
** [[GBrowse Balloon Tips|Balloon Tips]]
+
* [[GBrowse Persistent Variables]]
+
* [[GBrowse img]]
+
* [[Glyphs and Glyph Options]]
+
* [[RubberBandSelection|Rubber Band Selection]]
+
* [[Gbrowse Benchmarking]]
+
* [[GBrowse User Uploads]]
+
  
===POD documentation===
+
==Add some tracks==
  
There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod.
+
[Genes]
 +
feature      = gene
 +
glyph        = gene
 +
ignore_sub_part = polypeptide
 +
#bgcolor      = yellow
 +
forwardcolor = yellow
 +
reversecolor = turquoise
 +
label        = sub { my $f = shift;
 +
                    my $name = $f->display_name;
 +
                    my @aliases = sort $f->attributes('Alias');
 +
                    $name .= " (@aliases)" if @aliases;
 +
                    $name;
 +
  }
 +
height      = 6
 +
description  = 0
 +
key          = Named gene
 +
 +
[CDS]
 +
feature      = mRNA
 +
glyph        = cds
 +
description  = 0
 +
ignore_sub_part = polypeptide exon
 +
height      = 26
 +
sixframe    = 1
 +
label        = sub {shift->name . " reading frame"}
 +
key          = CDS
 +
citation    = This track shows CDS reading frames.
 +
 +
[repeats]
 +
feature      = match:repeatmasker
 +
glyph        = generic
 +
bgcolor      = black
 +
key          = Repeats
 +
 +
[ests]
 +
feature      = expressed_sequence_match
 +
glyph        = segments
 +
stranded    = 1
 +
bgcolor      = green
 +
key          = EST matches
 +
 +
[proteins]
 +
feature      = protein_match
 +
glyph        = segments
 +
stranded    = 1
 +
bgcolor      = pink
 +
fgcolor      = red
 +
key          = protein matches
 +
 +
[CoverageXyplot]
 +
feature        = coverage
 +
glyph          = wiggle_xyplot
 +
database      = bam_sample
 +
height        = 50
 +
fgcolor        = black
 +
bicolor_pivot  = 20
 +
pos_color      = blue
 +
neg_color      = red
 +
key            = Coverage (xyplot)
 +
 +
[Reads]
 +
feature        = match
 +
glyph          = segments
 +
draw_target    = 1
 +
show_mismatch  = 1
 +
mismatch_color = red
 +
database      = bam_sample
 +
bgcolor        = blue
 +
fgcolor        = white
 +
height        = 5
 +
label density  = 50
 +
bump          = fast
 +
key            = Reads
 +
 +
[Pair]
 +
feature      = read_pair
 +
glyph        = segments
 +
database      = bam_sample
 +
draw_target  = 1
 +
show_mismatch = 1
 +
bgcolor      = sub {
 +
                my $f = shift;
 +
                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
 +
                }
 +
fgcolor      = green
 +
height        = 3
 +
label        = sub {shift->display_name}
 +
label density = 50
 +
bump          = fast
 +
connector    = dashed
 +
balloon hover = sub {
 +
                my $f    = shift;
 +
                return '' unless $f->type eq 'match';
 +
                return 'Read: '.$f->display_name.' : '.$f->flag_str;
 +
                }
 +
key          = Read Pairs
  
GBrowse 2.x pod documents can also be viewed online at CPAN:
+
==Add our new database to the GBrowse.conf==
  
* [http://search.cpan.org/dist/GBrowse/docs/pod/FAQ.pod FAQ]
+
To let GBrowse know that there is a new database available, we have to add a few lines to GBrowse.conf. Add this to the bottom:
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.pod INSTALL]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/INSTALL.MacOSX.pod INSTALL.MacOSX]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-chado.pod README-chado]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-gff-files.pod README-gff-files] (see also [[GFF]])
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/README-lucegene.pod README-lucegene]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/BIOSQL_ADAPTER_HOWTO.pod BIOSQL_ADAPTER_HOWTO]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/GENBANK_HOWTO.pod GENBANK_HOWTO]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/PLUGINS_HOWTO.pod PLUGINS_HOWTO]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod DAS_HOWTO]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/MAKE_IMAGES_HOWTO.pod MAKE_IMAGES_HOWTO]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/GBROWSE_IMG.pod GBROWSE_IMG]
+
* [http://search.cpan.org/dist/GBrowse/docs/pod/ORACLE_AND_POSTGRESQL.pod ORACLE_AND_POSTGRESQL]
+
  
==Publications, Tutorials, and Presentations==
+
[pythium]
 +
description  = Pythium ultimum
 +
path          = pythium.conf
  
===Publications on or mentioning GBrowse===
+
===Updating SAMtools===
  
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:19957275/>
+
The version of SAMtools may need to be updated. Get the samtools release:
* SNP@Evolution: a hierarchical database of positive selection on the human genome. <ref name=PMID:19732458/> ([[GBrowse]]-related)
+
* TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <ref name=PMID:19683474/> ([[GBrowse]]-related)
+
* FishMap: a community resource for zebrafish genomics. <ref name=PMID:18554176/> ([[GBrowse]]-related)
+
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:18428797/>
+
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/>  (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].)
+
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/>
+
* The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]
+
  
===Tutorials===
+
  cd ~/Documents/Software
 +
  wget -O samtools-0.1.13.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.13/samtools-0.1.13.tar.bz2/download
 +
  tar jxvf samtools-0.1.13.tar.bz2
 +
  cd samtools-0.1.13
 +
  make
  
*[http://search.cpan.org/dist/GBrowse/htdocs/tutorial/tutorial.html Administration tutorial]
+
Install Bio::DB::Sam:
*[http://search.cpan.org/dist/GBrowse/htdocs/general_help.html Usage tutorial]
+
*[[GBrowse_Tutorial|Links to numerous GBrowse tutorials]]
+
* [http://www.openhelix.com/gbrowse Usage tutorial @ openhelix.com] - n.b. [[GBrowse 1.x]] tutorial
+
  
==Contacts and Mailing Lists==
+
  sudo cpan
 +
  cpan> install Bio::DB::Sam
  
{| class="wikitable"
+
when asked "Please enter the location of the bam.h and compiled libbam.a files:", answer:
|
+
 
! Mailing List Link
+
  /home/gmod/Documents/Software/samtools-0.1.13
! Description
+
 
! Archive(s)
+
==Add semantic zooming for the BAM tracks==
|-
+
 
! rowspan="2" | [[GBrowse]] & [[GBrowse_syn]]
+
Not doing this for very dense data (like BAM) is probably the number one performance killers for GBrowse; asking GBrowse to draw a track that has thousands of glyphs is time consuming (and ultimately, probably not very informative).
| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse gmod-gbrowse]
+
 
| [[GBrowse]] and [[GBrowse_syn]] users and developers.
+
[Reads:5001]
| [http://dir.gmane.org/gmane.science.biology.gmod.gbrowse Gmane], [http://gmod.827538.n3.nabble.com/GBrowse-f815907.html Nabble (2010/05+)], [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse Sourceforge]
+
feature        = coverage
|-
+
glyph          = wiggle_density
| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-cmts gmod-gbrowse-cmts]
+
height        = 15
| Code updates.
+
| [http://sourceforge.net/mailarchive/forum.php?forum_name=gmod-gbrowse-cmts Sourceforge]
+
[Pair:5001]
|}
+
feature        = coverage
 +
glyph          = wiggle_density
 +
height        = 15
 +
bgcolor        = purple
 +
 
 +
==Add "show summary" functionality==
 +
 
 +
For other tracks, when zoomed way out (100kb or 1MB), performance can similarly suffer, with a decreasing "information" content. Newer versions of GBrowse provide the ability to automatically generate density plots when zoomed out. This functionality is available from Chado and {{CPAN|Bio::DB::SeqFeature::Store}} data adaptors. To prepare our Chado database to do this semantic zooming, we need to run a script that comes with Bio::DB::Das::Chado:
 +
 
 +
  cd ~/Documents/Software/gbrowse-adaptors/Chado
 +
  svn update
 +
  perl bin/gmod_create_summary_statistics.pl
 +
 
 +
and then add to the pythium.conf file, somewhere near the top (ie, not in the track definitions):
  
Please report bugs to the [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291 SourceForge Bug Tracker] (select 'Category: Gbrowse').
+
  show summary = 99999
  
==GBrowse in the wild==
+
==Enabling full text searching==
  
Public installations of GBrowse:
+
If we try searching for "<tt>gene 7.92</tt>", we'll get "Not Found" as a result, even though genemark-scf1117875582023-abinit-gene-7.92 does exist. To look for partial strings, we need to enable full text searching. To do so, we need to run another script that comes with Bio::DB::Das::Chado:
*[http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase]
+
*[http://flybase.org/cgi-bin/gbrowse/dmel FlyBase]
+
*[http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse HapMap]
+
  
==See also==
+
  perl /home/gmod/Documents/Software/gbrowse-adaptors/Chado/bin/gmod_chado_fts_prep.pl
  
[[WebGBrowse]]
+
This does several things (including poorly estimating how long it will take to finish), including creating materialized views, using a tool provided by [[gmod:Category:SGN|SOL Genomics Network (SGN)]].  In practice, it would be a good idea to read the documentation of <tt>gmod_materialized_view_tool.pl</tt> for information on keeping the view up to date.
  
==More on GBrowse==
+
We also have to tell GBrowse that this Chado database can now do full text searching, by adding this to the Chado database stanza:
  
See [[:Category:GBrowse]]
+
  -fulltext 1
  
The [[:Image:GBrowseLogo.png|GBrowse logo]] was created by [mailto:alexisnb1@yahoo.com Alex Read], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].
+
Now we can search for "<tt>gene 7.92</tt>" and we'll find our gene (plus it's mRNA and exons) and we can click on the gene to see it in GBrowse.
  
 +
= Evaluation =
  
<references />
+
{{Feedback}}
  
[[Category:GBrowse]]
+
{{NextSession|Apollo|Apollo}}
[[Category:GMOD Components]]
+

Revision as of 18:43, 11 March 2011

Template:SessionHead

GBrowse Session

2011 GMOD Spring Training
8-12 March 2011
Scott Cain

{{#icon: GBrowseLogo.png|GBrowse|200|gmod:GBrowse}}


Prerequisites

Installed before using apt or cpan.

Install GBrowse

Easily installed via the cpan shell:

 sudo cpan
 cpan> install Bio::Graphics::Browser2

Which gets all of the prereqs that aren't installed on the machine.

Tutorial

Go to http://localhost/gbrowse2

Basic Chado Configuration (if we have time)

Bio::DB::Das::Chado was installed when we created the image. Sample configuration files are available with GBrowse, and we'll get the sample Chado file:

 wget http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/contrib/conf_files/07.chado.conf -O pythium.conf


Some simple tweaks and additions:

  • Change description
  • Get rid of database = main
  • Remove or change examples (yeast examples don't help anybody)
  • Add initial landmark (initial landmark = scf1117875582023)

DB connection info

[annotation:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado
                -user gmod
                -inferCDS 1
                -srcfeatureslice 1
search options = default

Add a BAM data source

[bam_sample:database]
db_adaptor     = Bio::DB::Sam
db_args        = -fasta /var/www/gbrowse2/databases/pythium/scf1117875582023.fasta
                 -bam   /var/www/gbrowse2/databases/pythium/simulated-sorted.bam
search options = default

Add track defaults

[TRACK DEFAULTS]
glyph       = generic
database    = annotation
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100

Note particularly the "database" entry--for most tracks we'll be using the annotation database, but the bam_sample data source will be available when we want it.

Add some tracks

[Genes]
feature      = gene
glyph        = gene
ignore_sub_part = polypeptide
#bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
label        = sub { my $f = shift;
                    my $name = $f->display_name;
                    my @aliases = sort $f->attributes('Alias');
                    $name .= " (@aliases)" if @aliases;
                    $name;
  }
height       = 6
description  = 0
key          = Named gene

[CDS]
feature      = mRNA
glyph        = cds
description  = 0
ignore_sub_part = polypeptide exon
height       = 26
sixframe     = 1
label        = sub {shift->name . " reading frame"}
key          = CDS
citation     = This track shows CDS reading frames.

[repeats]
feature      = match:repeatmasker
glyph        = generic
bgcolor      = black
key          = Repeats

[ests]
feature      = expressed_sequence_match
glyph        = segments
stranded     = 1
bgcolor      = green
key          = EST matches

[proteins]
feature      = protein_match
glyph        = segments
stranded     = 1
bgcolor      = pink
fgcolor      = red
key          = protein matches

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
database       = bam_sample
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = blue
neg_color      = red
key            = Coverage (xyplot)

[Reads]
feature        = match
glyph          = segments
draw_target    = 1
show_mismatch  = 1
mismatch_color = red
database       = bam_sample
bgcolor        = blue
fgcolor        = white
height         = 5
label density  = 50
bump           = fast
key            = Reads 

[Pair]
feature       = read_pair
glyph         = segments
database      = bam_sample
draw_target   = 1
show_mismatch = 1
bgcolor       = sub {
                my $f = shift;
                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
                }
fgcolor       = green
height        = 3
label         = sub {shift->display_name}
label density = 50
bump          = fast
connector     = dashed
balloon hover = sub {
                my $f     = shift;
                return  unless $f->type eq 'match';
                return 'Read: '.$f->display_name.' : '.$f->flag_str;
                }
key           = Read Pairs

Add our new database to the GBrowse.conf

To let GBrowse know that there is a new database available, we have to add a few lines to GBrowse.conf. Add this to the bottom:

[pythium]
description   = Pythium ultimum
path          = pythium.conf

Updating SAMtools

The version of SAMtools may need to be updated. Get the samtools release:

 cd ~/Documents/Software
 wget -O samtools-0.1.13.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.13/samtools-0.1.13.tar.bz2/download
 tar jxvf samtools-0.1.13.tar.bz2
 cd samtools-0.1.13
 make

Install Bio::DB::Sam:

 sudo cpan
 cpan> install Bio::DB::Sam

when asked "Please enter the location of the bam.h and compiled libbam.a files:", answer:

 /home/gmod/Documents/Software/samtools-0.1.13

Add semantic zooming for the BAM tracks

Not doing this for very dense data (like BAM) is probably the number one performance killers for GBrowse; asking GBrowse to draw a track that has thousands of glyphs is time consuming (and ultimately, probably not very informative).

[Reads:5001]
feature        = coverage
glyph          = wiggle_density
height         = 15

[Pair:5001]
feature        = coverage
glyph          = wiggle_density
height         = 15
bgcolor        = purple

Add "show summary" functionality

For other tracks, when zoomed way out (100kb or 1MB), performance can similarly suffer, with a decreasing "information" content. Newer versions of GBrowse provide the ability to automatically generate density plots when zoomed out. This functionality is available from Chado and Bio::DB::SeqFeature::Store data adaptors. To prepare our Chado database to do this semantic zooming, we need to run a script that comes with Bio::DB::Das::Chado:

 cd ~/Documents/Software/gbrowse-adaptors/Chado
 svn update
 perl bin/gmod_create_summary_statistics.pl

and then add to the pythium.conf file, somewhere near the top (ie, not in the track definitions):

 show summary = 99999

Enabling full text searching

If we try searching for "gene 7.92", we'll get "Not Found" as a result, even though genemark-scf1117875582023-abinit-gene-7.92 does exist. To look for partial strings, we need to enable full text searching. To do so, we need to run another script that comes with Bio::DB::Das::Chado:

 perl /home/gmod/Documents/Software/gbrowse-adaptors/Chado/bin/gmod_chado_fts_prep.pl

This does several things (including poorly estimating how long it will take to finish), including creating materialized views, using a tool provided by SOL Genomics Network (SGN). In practice, it would be a good idea to read the documentation of gmod_materialized_view_tool.pl for information on keeping the view up to date.

We also have to tell GBrowse that this Chado database can now do full text searching, by adding this to the Chado database stanza:

 -fulltext 1

Now we can search for "gene 7.92" and we'll find our gene (plus it's mRNA and exons) and we can click on the gene to see it in GBrowse.

Evaluation

Please give us your comments on this session. We will ask for your feedback on each session and the course as a whole on the last day. Your comments will help guide the direction and content of future GMOD training and outreach efforts.


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Facts about "GBrowse"RDF feed
Available on platformweb +
Has URLhttp://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, https://github.com/GMOD/GBrowse +, http://gbrowse.org +, http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, http://flybase.org/cgi-bin/gbrowse/dmel + and http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +
Has descriptionGBrowse is a combination of database and iGBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)
Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.
is required and a single database is used. +
Has development statusinactive +
Has full nameGeneric Genome Browser +
Has input formatGFF3 + and GFF2 +
Has licenceGPL2 + and Artistic License +
Has logoGBrowseLogo.png +
Has software maturity statusmature +
Has support statusinactive +
Has titleWormBase +, FlyBase + and HapMap +
Has topicGBrowse +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Release date1 January 2001 +
Tool functionality or classificationGenome Visualization & Editing +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.GBrowse#http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, GBrowse#https://github.com/GMOD/GBrowse +, GBrowse#http://gbrowse.org +, GBrowse#http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, GBrowse#http://flybase.org/cgi-bin/gbrowse/dmel + and GBrowse#http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +