GBrowse syn

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The Generic Synteny Browser

{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}
GBrowse_syn, as implemented at WormBase

GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species.  It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later).  Working examples can be seen at TAIR, WormBase, and SGN.

If you use GBrowse_syn in for a publication, please cite:

McKay SJ, Vergara IA and Stajich, J. 2010. "Using the Generic Synteny Browser (Gbrowse_syn)" in Current Protocols in Bioinformatics (Wiley Interscience) doi: 10.1002/0471250953.bi0912s31


Notes on Whole Genome Alignment Data

The focus of this documentation is on the GBrowse_syn application. However, how to generate whole genome alignments, identify orthologous regions, etc, are the subject of considerable interest, so some background reading is listed below:

Installation

  • GBrowse_syn uses much of the same infrastructure as GBrowse, in terms of species databases, configuration files, perl libraries, etc.
  • It comes as part of the GBrowse distribution, version 1.69 and later (GBrowse installation info...).
  • It differs in that databases and configuration for individual species are linked together via a central configuration file and a joining database that contains reciprocal alignments between all species represented in the browser.
  • We recommend using the most up-to-date version of the application (v. 1.7 or later) either with the GBrowse netinstall script (use the -d option) or with a source code installation from SVN.

Configuration

  • Configuration of GBrowse_syn is much the same as for GBrowse, with database and display options controlled by a configuration file
  • GBrowse_syn uses a main configuration file for general options plus an individual configuration for each species represented in the mutliple sequence alignments
  • Details....

The Alignment data

  • GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
  • There is an additional GBrowse database for each species represented in the alignments
  • The species' databases are configured in the same way as a regular GBrowse installations
  • Details...

User interface

  • The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data.
  • GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
  • There is no upward limit of the number of species that can be displayed.
  • Details...

Support

Mailing List Link Description Archive(s)
GBrowse & GBrowse_syn gmod-gbrowse GBrowse and GBrowse_syn users and developers. Gmane, Nabble (2010/05+), Sourceforge
gmod-gbrowse-cmts Code updates. Sourceforge

Development

See the discussion page for notes on developing GBsyn (as it is affectionately abbreviated).

Presentations and Workshops

The GBrowse_syn logo was created by Darek Lakey, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.