GBrowse syn

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GBrowse_syn running on WormBase
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.


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:

Documentation

There is a session
on Gbrowse_syn at
2009 GMOD Summer School - Europe

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