Difference between revisions of "GBrowse"

Revision as of 22:10, 16 April 2007

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.

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 stable 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

• Easy Internet-based installer
  • Save the above link to your home directory as gbrowse_netinstall.pl, and then run "perl gbrowse_netinstall.pl". You will need to be logged in as the adminstrator (or run "sudo") to do this step.
• Detailed step-by-step install documentation
  • Install on MacOSX
  • Install on Linux
  • Install on Windows
  • Install on Ubuntu

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.