GBrowse
The Generic Genome Browser (which is also occationally and incorrectly referred to as 'gbrowser') is a combination of database and interactive web page for manipulating and displaying annotations on genomes. The web browser has the following features.
- Simultaneous bird's eye and detailed views of the genome.
- Scroll, zoom, center.
- 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.
Contents
Tutorial
Scan through /nondrupal/tutorial/tutorial.html the tutorial that comes with the package to get a quick overview of its features.
Downloading and Installing
Download the source from the SourceForge download page., or see the installation instructions for information on installing from a binary distribution (most suitable on MS Windows platforms).
Getting the Latest & Greatest Version by CVS
There are many new features in the current development version which have not been released yet. To get the latest and greatest version, please use anonymous CVS. The recommended branch to use is "gbrowse-sessions" which is more stable than HEAD. Here is the recipe:
% cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login CVS password: <hit return> % cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r gbrowse-session Generic-Genome-Browser
Once you have successfully checked out the Generic-Genome-Browser distribution, you can simply perform a "cvs update" inside the directory to get recent changes.
You can also browse the GBrowse CVS here.
Demo
Select an organism and desired region; then press "Browse." This will take you to a live demo where you can browse the genomes of worm, yeast and fly. Mouse will be added when the assembly is published.
Browsable Genomes | |||
---|---|---|---|
C. elegans (worm) | D. melanogaster (fly) | ||
Chromosome I |
Arm 2L | ||
S. cerevisiae (yeast) | H. sapiens (human) | ||
Chromosome I |
Chromosome 1 |
About the Database
GBrowse has a flexible adaptor system for running off various types of database. Standard adaptors include:
- Flat file adaptors (in-memory, indexed) -- put your annotations in a directory and go!
- Relational database adaptors -- Chado, Bio::DB::GFF, BioSQL
- Network adaptors -- read annotations from GenBank, UCSC or Ensembl
Getting the Software
This is Open Source software, which is available for your own genome annotation projects. To get it, go to the SourceForge download page. Please report bugs to the SourceForge bug tracker. Please send questions to the GBrowse mailing list.
Available on platform | web + |
Has URL | http://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 description | GBrowse is a combination of database and i … GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
|
Has development status | inactive + |
Has full name | Generic Genome Browser + |
Has input format | GFF3 + and GFF2 + |
Has licence | GPL2 + and Artistic License + |
Has logo | GBrowseLogo.png + |
Has software maturity status | mature + |
Has support status | inactive + |
Has title | WormBase +, FlyBase + and HapMap + |
Has topic | GBrowse + |
Is open source | Yes + |
Link type | download +, source code +, website + and wild URL + |
Release date | 1 January 2001 + |
Tool functionality or classification | Genome Visualization & Editing + |
Written in language | Perl + |
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 + |