Difference between revisions of "GBrowse syn"
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Revision as of 18:52, 8 October 2012
- Mature release
- active support
- 1 About Generic Synteny Browser (GBrowse_syn)
- 2 Downloads
- 3 Using GBrowse_syn
- 4 Publications, Tutorials, and Presentations
- 5 Contacts and Mailing Lists
- 6 GBrowse_syn in the wild
- 7 GBrowse_syn Development
- 8 See also
- 9 More on GBrowse_syn
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).
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.
See the help for GBrowse_syn
- 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
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) 
- 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.
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|
GBrowse_syn in the wild
Public installations of GBrowse_syn:
See the discussion page for notes on further GBrowse_syn development.
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:
- Primer on Hierarchical Genome Alignment Strategies
- article on PECAN and ENREDO
- all about PECAN
- Information about EnsEMBL's compara pipeline
More on GBrowse_syn
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