- Mature release
- Active development
- Active support
The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. For a demo of its features, see WormBase, FlyBase, or Human Genome Segmental Duplication Database and others.
- 1 Description
- 2 GBrowse Versions
- 3 Installation
- 4 Documentation
- 5 Downloads
- 6 About Databases
- 7 Email Threads
- 8 Contacts
- 9 Logo
- 10 References
- 11 See Also
GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Some of its 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)
GBrowse 1.X (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.
GBrowse is Perl-based. It 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. See the step-by-step instructions below for detailed instructions:
- Install on MacOSX
- Install on Windows
- Install on Ubuntu and other Debian-based systems
- Install on Fedora Core and other RPM-based systems
- Install on Gentoo Linux system
- Source Code Install (for other Linux systems)
|GBrowse 1.x||GBrowse 2.0|
|Configure||Wiki / Tutorial||Wiki / Tutorial|
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:
- README-gff-files.pod (see also GFF)
Since these are in Perl POD format these files may contain formatting code when viewed in a Web browser.
Source Code Download (tar.gz file)
Download the source from the SourceForge download page.
Net-based Installer Script
The net installer script, called gbrowse_netinstall.pl at the GBrowse GitHub repository will automatically download and install GBrowse and its Perl libraries for you. See Installation for details on using this script.
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There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use GitHub. The recommended branch to use is master, which is usually stable:
git clone git://github.com/GMOD/GBrowse.git
or, if you have commit priveleges on the GBrowse repository, you can use:
git clone firstname.lastname@example.org:GMOD/GBrowse.git
which downloads significantly faster.
Once you have successfully cloned the GBrowse repository, fetch recent changes by executing
git pull inside the
You can also browse the GBrowse GitHub repository.
1.x Development Version
The link above will get you to the GBrowse2 development version. To get to the GBrowse 1.x development branch, use the stable branch:
git clone https://github.com/GMOD/GBrowse.git cd GBrowse git checkout -t -b stable origin/stable
- Git Terminology guide (80% generic, 20% parrot specific).
- Git Workflow guide (80% generic, 20% parrot specific).
GBrowse has a flexible adaptor (yes, it is spelled that way and is not "adapter") system for running off various types of databases/sources. A common question is "which adaptor should I be using?" This attempts to answer that question.
|Adaptor||Other required software||Roughly how many users||Pros||Cons|
|Bio::DB::SeqFeature::Store (use bp_seqfeature_load.pl)||MySQL, PostgreSQL, SQLite, BerkeleyDB||Many and growing fast.||Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with GFF3||Developed for use with GFF3; about 2X slower than Bio::DB::GFF to load a database|
|Bio::DB::GFF (use bp_load_gff.pl, bp_bulk_load_gff.pl, bp_fast_load_gff.pl)||A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB||Lots! (Especially MySQL)||Quite fast; large user base; Have to use this if your data is in the (now deprecated) GFF2 format.||Does not work well with GFF3 formatted data|
|Bio::DB::Sam (available from CPAN)||SAMtools||Growing (particularly with GBrowse2)||Very fast access to NextGen sequencing data||Difficult to use with GBrowse 1.70|
|Bio::DB::BigWig and Bio::DB::BigWigSet (available from CPAN)||UCSC Formats||Growing (particularly with GBrowse2)||Very fast access to data in bigWig format||Difficult to use with GBrowse 1.70|
|Bio::DB::BigBed (available from CPAN)||UCSC Formats||Growing (particularly with GBrowse2)||Very fast access to data in bigBed format||Difficult to use with GBrowse 1.70|
|Bio::DB::Das::Chado (available from CPAN)||PostgreSQL and a Chado schema||Relatively few due to the specialized nature of Chado||Allows 'live' viewing of the features in a Chado database||Slow compared to Bio::DB::GFF|
|Bio::DB::Das::BioSQL (available from CPAN)||MySQL and a BioSQL schema||Relatively few due to the small number of BioSQL users||Allows 'live' viewing of the features in a BioSQL database||Slow compared to Bio::DB::GFF|
|Memory (ie, flat file database using either Bio::DB::GFF or SeqFeature::Store)||None||For real servers, none||Easy for rapid development and testing||Very slow for more than a few thousand features|
|LuceGene||Lucene (searches indexed flat files)||Relatively few|
There have been some useful email threads on adaptor choices and tradeoffs.
- Memory Database, 2010/06
Please report bugs to the SourceForge Bug Tracker (select 'Category: Gbrowse').
|Mailing List Link||Description||Archive(s)|
|GBrowse & GBrowse_syn||gmod-gbrowse||GBrowse and GBrowse_syn users and developers.||Gmane, Nabble (2010/05+), Sourceforge|
Installation and Setup
See also Category:GBrowse