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Revision as of 00:37, 2 February 2010

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The Generic Synteny Browser

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.

Status

• Mature release
• Active development
• Active support

Resources

• Alignment Primer
• Tutorial
• Configuration
• Help
• Example
• Mailing List
• 2008 SurveyTemplate:ComponentBoxEventsHeader

May 6-9

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:

• Primer on Hierarchical Genome Alignment Strategies
• article on PECAN and ENREDO
• all about PECAN
• Information about EnsEMBL's compara pipeline

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 (v. 1.7 or later) either with the GBrowse netinstall script (use the -d option) or with a source code installation from SVN.

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....

The Alignment data

• GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
• There is an additional GBrowse database for each species represented in the alignments
• The species' databases are configured in the same way as a regular GBrowse installations
• Details...

User interface

• The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data.
• GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
• There is no upward limit of the number of species that can be displayed.
• Details...

Presentations and Workshops

• Challenges in Comparative Genome Browsing - Presented by Sheldon McKay at the European Bioinformatics Institute, Hinxton, UK.
• Comparative Genomics with GBrowse_syn - Presentation by Sheldon McKay at the SMBE 2009 GMOD Workshop on using GBrowse_syn for comparative genomics.
• GBrowse_syn at PAG - Presentation by Sheldon McKay at the Plant and Animal Genomes meeting, San Diego, CA, USA.
• November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.