GBrowse syn

From GMOD

GBrowse_syn running on WormBase.org

GBrowse_syn is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It is included with the standard GBrowse package (version 1.69 and later). A working example can be seen at WormBase.

1 Documentation

Documentation

There are sessions
on Gbrowse_syn at

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