This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
- Beta release
- Development: active
- Support: active
- 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: https://github.com/GMOD/GBrowse
- 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.
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 multiple sequence alignments.
More information on GBrowse_syn configuration
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
<ref>tag; no text was provided for refs named
Cite error: Invalid
Raw tool data at GBrowse_syn/tool data
|Available on platform||web +|
|Has URL||https://github.com/GMOD/GBrowse +, http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri%3Bname=chrX:620000..670000 +, http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 +, http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele%3Bname=X:1050001..1150000 + and http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ +|
|Has description||GBrowse_syn, or the Generic Synteny Browse … 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). GBrowse package (version 1.69 and later). +|
|Has development status||active +|
|Has download URL||https://github.com/GMOD/GBrowse +|
|Has full name||Generic Synteny Browser +|
|Has logo||GBrowse_syn_logo.png +|
|Has software maturity status||beta release +|
|Has support status||active +|
|Has title||The Arabidopsis Information Resource +, WormBase + and Sol Genomics +|
|Has topic||GBrowse syn +|
|Is open source||Yes +|
|Link type||download +, source code +, demo server + and wild URL +|
|Release date||1 January 2007 +|
|Tool functionality or classification||Comparative genome visualization +|
|Written in language||Perl +|
|Has subobjectThis property is a special property in this wiki.||GBrowse syn#https://github.com/GMOD/GBrowse +, GBrowse syn +, GBrowse syn +, GBrowse syn + and GBrowse syn#http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ +|