View source for User:Girlwithglasses/Template:ToolData/gbrowse syn

<noinclude>
*[[User:Girlwithglasses/Template:ToolData/generic|Generic tool data]]
*[[User:Girlwithglasses/Template:StandardToolDisplay|tool template]]
</noinclude>

{{ {{{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 = <!-- http://tool_home.org -->
| 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).
| scrnsht = [[Image:GBrowse_syn.png||thumb|400px|GBrowse_syn, as implemented at WormBase]]
| public_server = 
| dl = <!-- GBrowse dl info -->
| dl_src = <!-- http://download.src.here.com -->
| dl_dev = <!-- http://download.dev.version.here.com -->
| 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 [[GBrowse_2.0_Install_HOWTO|installation instructions for GBrowse]].
| req = <!-- Any system requirements -->
| 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|GBrowse_syn configuration]]

| usage =
See the [[GBrowse_syn_Help|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
* [[GBrowse_syn_Database|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|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 = <!-- documentation links -->
| papers = <!-- publications -->
Please refer to the following paper when citing GBrowse_syn:

* Using the Generic Synteny Browser ([[GBrowse_syn]]) <ref name=PMID:20836076/>

| tutorials = <!-- interactive tutorials or workshops -->
*[[GBrowse_syn_Tutorial|Installing and configuring GBrowse_syn]]
| presentations = <!-- non-interactive tutorials or workshops -->
* [[:Media:GBrowse_syn_EBI2009.pdf|Challenges in Comparative Genome Browsing]] - Presented by [[User:Mckays|Sheldon McKay]] at the [http://www.ebi.ac.uk European Bioinformatics Institute], Hinxton, UK.
* [[:Media:GBrowse_synSMBE2009.pdf|Comparative Genomics with GBrowse_syn]] - Presentation by [[User:Mckays|Sheldon McKay]] at the [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE 2009 GMOD Workshop] on using [[GBrowse_syn]] for [[:Category:Comparative Genomics|comparative genomics]].
* [[GBrowse_syn PAG 2009 Workshop| GBrowse_syn at PAG]] - Presentation by [[User:Mckays|Sheldon McKay]] at the Plant and Animal Genomes meeting, San Diego, CA, USA.
* [[Media:Gbrowse_syn.pdf|November 2007]] - [[User:Mckays|Sheldon McKay]]'s presentation on GBrowse_syn at the [[November 2007 GMOD Meeting#GBrowse_Syn|November 2007 GMOD Meeting]].

| mail = Support is via the GBrowse mailing list:

{{MailingListsFor|GBrowse}}

| logo_info = 
The [[:Image:GBrowse_syn_logo.png|GBrowse_syn logo]] was created by [mailto:NextLevelDesignStudios@gmail.com Darek Lakey], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].
| wild_urls = 
*[http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 The Arabidopsis Information Resource]
*[http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 WormBase]
*[http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ Sol Genomics]

| dev_ppl = <!-- who is developing the tool? -->
| dev_status = See the [[{{TALKPAGENAME}}|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:
*[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577869/ article on PECAN and ENREDO]
*[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN]
*[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline]
}}