- Mature release
- Development: active
- Support: active
Taught at the 2013 GMOD Summer School
About Generic Genome Browser (GBrowse)
GBrowse 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.
Visit the GBrowse website.
- Download GBrowse: http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
- 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.
- GBrowse can also be found on CPAN and in the Debian sid ("unstable") apt package repository and can be installed via apt-get in Ubuntu 12.04 and later.
GBrowse is Perl-based and the GBrowse 2.x modules are 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.
- Configuration guide
- GBrowse Adaptors
- GBrowse Backends
- GBrowse FAQ
- Annotation Help
- GBrowse Persistent Variables
- GBrowse img
- Glyphs and Glyph Options
- Rubber Band Selection
- Gbrowse Benchmarking
- GBrowse User Uploads
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.
GBrowse 2.x pod documents can also be viewed online at CPAN:
- README-gff-files (see also GFF)
Publications, Tutorials, and Presentations
Publications on or mentioning GBrowse
- Using the Generic Genome Browser (GBrowse). 
- SNP@Evolution: a hierarchical database of positive selection on the human genome.  (GBrowse-related)
- TBrowse: an integrative genomics map of Mycobacterium tuberculosis.  (GBrowse-related)
- FishMap: a community resource for zebrafish genomics.  (GBrowse-related)
- Using the Generic Genome Browser (GBrowse). 
- Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains.  (See YSB.)
- Gbrowse Moby: a Web-based browser for BioMoby Services. 
- The generic genome browser (GBrowse): a building block for a model organism system database.  PDF
- GBrowse tutorial from 2012 GMOD Summer School
- Demonstrates setting up, configuring and using GBrowse with some sample data. GBrowse is provided on an Amazon Machine Image; see GMOD in the Cloud for more information on getting a GMOD AMI.
- GBrowse tutorial from 2010 GMOD Summer School
- Set up and run GBrowse with sample data. It provides a VMware image to work on, and relies heavily on the GBrowse2 Admin Tutorial.
- GBrowse2 Admin Tutorial
- Step by step guide on how to configure and load data into GBrowse. Administration tutorials are available for both the GBrowse2 Admin Tutorial, and the earlier 1.x versions.
- Usage tutorial
- GBrowse usage tutorial
- GBrowse NGS Tutorial
- Instructions on how to visualize next generation sequencing data in GBrowse using SAMtools. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
- GBrowse video tutorial
- Produced by EuPathDB; please direct praise and thanks to them!
- GBrowse User Tutorial at OpenHelix
- Demonstrates the GBrowse user interface. NB: this tutorial is for GBrowse 1.x
Contacts and Mailing Lists
|Mailing List Link||Description||Archive(s)|
|GBrowse & GBrowse_syn||gmod-gbrowse||GBrowse and GBrowse_syn users and developers.||Gmane, Nabble (2010/05+), Sourceforge|
Please report bugs to the Bug Tracker (select 'Category: Gbrowse').
GBrowse in the wild
Public installations of GBrowse:
More on GBrowse
- ↑ . Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics 2009 Chapter 9:Unit 9.9.
- ↑ , , , , and . SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evol. Biol. 2009 9:221.
DOI:10.1186/1471-2148-9-221 PMCID:PMC2755008 PMID:19732458
- ↑ , , , , and . TBrowse: an integrative genomics map of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2009 89:386-7.
- ↑ et al. FishMap: a community resource for zebrafish genomics. Zebrafish 2008 5:125-30.
- ↑ . Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics 2007 Chapter 9:Unit 9.9.
- ↑ et al. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2007 2:e322.
DOI:10.1371/journal.pone.0000322 PMCID:PMC1829191 PMID:17389913
- ↑ . Gbrowse Moby: a Web-based browser for BioMoby Services. Source Code Biol Med 2006 1:4.
DOI:10.1186/1751-0473-1-4 PMCID:PMC1636335 PMID:17147784
- ↑ et al. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 12:1599-610.
DOI:10.1101/gr.403602 PMCID:PMC187535 PMID:12368253
Raw tool data at GBrowse/tool data