Revision as of 21:56, 11 June 2009

GBrowse_syn running on WormBase.org

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.

Documentation

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 either with the GBrowse netinstall script (use the -d option) or with a source code installation.

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 of GBrowse_syn configuration can be found on this page.

The Alignment data

• GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
• There is an additional database for each species represented in the alignments
• The species' databases are configured in the same way as a regular GBrowse installation
• Detailed information about the alignment database can be found on this page

User interface

• GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
• Details of the user interface can be found on this page

Presentations and Workshops

• Comparative Genomics with GBrowse_syn - Presentation by Sheldon McKay at the SMBE 2009 GMOD Workshop on using GBrowse_syn for comparative genomics.
• GBrowse_syn PAG 2009 Workshop
• November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.