GBrowse syn

GBrowse_syn running on WormBase.org
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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 --dev 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 database

• 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 normal GBrowse data sources
• Detailed informatio about the alignment database can be found on this page

Example alignment database To get an idea of how alignment database is built, the files and scripts used to load the synteny browser at WormBase can be obtained from the WormBase ftp site.

User interface

• Help with the user interface can be found on this page

Presentations

• November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.