GBrowse
Contents
Description
GBrowse is the most popular viewer in GMOD. For a list of GBrowse and GMOD installations see the GMOD Users page.
The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes. Some of its 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.
- 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)
Documentation
- Generic-Genome-Browser/docs/tutorial/tutorial.html
- Generic-Genome-Browser/htdocs/general_help.html
- Generic-Genome-Browser/htdocs/annotation_help.html
- GBrowse FAQ
In addition there are many useful HTML files that are created for you when you install the package, including:
- Generic-Genome-Browser/docs/pod/BIOSQL_ADAPTER_HOWTO.pod
- Generic-Genome-Browser/docs/pod/GENBANK_HOWTO.pod
- Generic-Genome-Browser/docs/pod/PLUGINS_HOWTO.pod
- Generic-Genome-Browser/docs/pod/CONFIGURE_HOWTO.pod
- Generic-Genome-Browser/docs/pod/INSTALL.MacOSX.pod
- Generic-Genome-Browser/docs/pod/README-berkeley-gadfly.pod
- Generic-Genome-Browser/docs/pod/DAS_HOWTO.pod
- Generic-Genome-Browser/docs/pod/INSTALL.pod
- Generic-Genome-Browser/docs/pod/README-chado.pod
- Generic-Genome-Browser/docs/pod/FAQ.pod
- Generic-Genome-Browser/docs/pod/MAKE_IMAGES_HOWTO.pod
- Generic-Genome-Browser/docs/pod/README-gff-files.pod
- Generic-Genome-Browser/docs/pod/GBROWSE_IMG.pod
- Generic-Genome-Browser/docs/pod/ORACLE_AND_POSTGRESQL.pod
- Generic-Genome-Browser/docs/pod/README-lucegene.pod
Since these are in Perl POD format these files may contain formatting code when viewed in a Web browser.
Downloads
Download the source from the SourceForge download page.
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 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.
Installation
About Databases
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, BioSQL.
- Network adaptors -- read annotations from GenBank, UCSC or Ensembl.
- GFF databases -- Bio::DB::GFF, Bio::DB::SeqFeature
Contacts
Please report bugs to the SourceForge Bug Tracker.
Please send questions to the GBrowse mailing list.