GBrowse syn
GBrowse_syn is a synteny browser derived from GBrowse. It has many of the same zoom, pan and other genome navigation options as GBrowse. It designed as a synteny browser for three or more genomes. A working example can be seen at WormBase.
Contents
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 HOWTO...).
- 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.
Example alignment database
The files and scripts used to load the synteny browser at WormBase can be obtained from the WormBase ftp site.
Configuration
Configuration files
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. This file ends with the extension ".synconf". Below is the configuration file used by WormBase.
The species configuration file contains information used by each species-specific database. This file has the extension ".syn". To avoid confusing GBrowse, select names for your GBrowse_syn configuration files that are not similar to the names or regular GBrowse configuration files. The configuration file used for C. briggsae on wormbase is shown below.
The Alignment database
Presentations
- November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.