User:Girlwithglasses/Template:ToolData/gbrowse syn
{{ {{{template}}}
| name = GBrowse_syn
| status = mature
| dev = active?
| support = active
| os_web = yes
| os_mac = yes
| os_linux = yes
| os_win = yes
| os_unix = yes
| logo = GBrowse_syn_logo.png
| home =
| about = 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).
| public_server = | dl = | dl_src = | dl_dev = | getting_started_preamble = 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. | req = | install = | config = 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.
More information on GBrowse_syn configuration
| usage = 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.
| doc = | papers = Please refer to the following paper when citing GBrowse_syn:
- Using the Generic Synteny Browser (GBrowse_syn) [1]
| tutorials =
| presentations =
- 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.
| mail = 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 |
| logo_info = 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. | wild_urls =
| dev_ppl = | dev_status = See the discussion page for notes on further GBrowse_syn development. | tool_type =
- Comparative Genome Visualization
| formats = | 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:
- Primer on Hierarchical Genome Alignment Strategies
- article on PECAN and ENREDO
- all about PECAN
- Information about EnsEMBL's compara pipeline
}}
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