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Revision as of 21:43, 13 February 2013


GBrowse_syn logo
Status
  • Mature release
  • maintenance
  • active support
Resources

About Generic Synteny Browser (GBrowse_syn)

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).


Screenshots

GBrowse_syn, as implemented at WormBase

Downloads

Download GBrowse_syn: http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/


The development version of GBrowse_syn is found at https://github.com/GMOD/GBrowse. Please be aware that development versions may have new features that are not fully tested.

Using GBrowse_syn

GBrowse_syn has been part of the GBrowse distribution since version 1.69; we recommend using the most up-to-date version of GBrowse 2. Please follow the installation instructions for GBrowse.

Documentation

See the help for GBrowse_syn

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 databases for each species are configured in the same way as a regular GBrowse installations
  • Details on the GBrowse_syn database

User interface

The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data (see the screenshot above).

GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species. There is no upper limit to the number of species that can be displayed.

Publications, Tutorials, and Presentations

Publications on or mentioning GBrowse_syn

Please refer to the following paper when citing GBrowse_syn:

  • Using the Generic Synteny Browser (GBrowse_syn) [1]

Tutorials

Presentations

Contacts and Mailing Lists

Support is via the GBrowse mailing list:

Mailing List Link Description Archive(s)
GBrowse & GBrowse_syn gmod-gbrowse GBrowse and GBrowse_syn users and developers. Gmane, Nabble (2010/05+), Sourceforge
gmod-gbrowse-cmts Code updates. Sourceforge


GBrowse_syn in the wild

Public installations of GBrowse_syn:

GBrowse_syn Development

See the discussion page for notes on further GBrowse_syn development.


See also

The focus of this documentation is the GBrowse_syn application. However, the generation of whole genome alignments and identification of orthologous regions are the subject of considerable interest, so some background reading is listed below:

More on GBrowse_syn

See Category:GBrowse_syn The GBrowse_syn logo was created by Darek Lakey, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.


  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20836076