Difference between revisions of "GBrowse syn/tool data"

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(GBrowse syn tool data)
 
m (Updating info and format)
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| name = GBrowse_syn
 
| name = GBrowse_syn
 
| full_name = Generic Synteny Browser
 
| full_name = Generic Synteny Browser
| status = Mature release
+
| status = beta
| dev = maintenance
+
| dev = active
| os = web, mac, win, linux, unix
+
| support = active
 +
| type = Comparative genome visualization
 +
| os_web = y
 
| logo = GBrowse_syn_logo.png
 
| logo = GBrowse_syn_logo.png
 
| home =  
 
| home =  
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| public_server =  
 
| public_server =  
 
| dl =  
 
| dl =  
| dl_url = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/
+
| dl_url = https://github.com/GMOD/GBrowse
 
| dl_src =  
 
| dl_src =  
 
| dl_src_url =  
 
| dl_src_url =  
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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.
 
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.
 
| papers = Please refer to the following paper when citing GBrowse_syn:
 
| papers = Please refer to the following paper when citing GBrowse_syn:
 
 
* Using the Generic Synteny Browser (GBrowse_syn) <ref name=PMID:20836076/>
 
* Using the Generic Synteny Browser (GBrowse_syn) <ref name=PMID:20836076/>
 
| presentations = * [[: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.
 
| presentations = * [[: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.
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* [[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.
 
* [[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]].
 
* [[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]].
| tutorials = *[[GBrowse_syn_Tutorial|Installing and configuring GBrowse_syn]]
+
| tutorials =  
 +
;[[GBrowse_syn_Tutorial]]
 +
:Installing and configuring GBrowse_syn
 
| wild_urls = *[http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 The Arabidopsis Information Resource]
 
| 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://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 WormBase]
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| dev_ppl =  
 
| dev_ppl =  
 
| dev_status = See the [[{{TALKPAGENAME}}|discussion page]] for notes on further GBrowse_syn development.
 
| dev_status = See the [[{{TALKPAGENAME}}|discussion page]] for notes on further GBrowse_syn development.
| contact_email =  
+
| contact_email = [mailto:mckays@cshl.edu Sheldon Mckay]
| formats =  
+
| input =
 +
| output =
 
| 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:
 
| 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.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies]
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*[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN]
 
*[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]
 
*[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline]
| demo_server =  
+
| demo_server = http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000
 
| survey_link = GBrowse_syn
 
| survey_link = GBrowse_syn
 
}}
 
}}

Revision as of 16:41, 15 February 2013

{{ {{{template}}} | name = GBrowse_syn | full_name = Generic Synteny Browser | status = beta | dev = active | support = active | type = Comparative genome visualization | os_web = y | 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).

| screenshot =
GBrowse_syn, as implemented at WormBase

| public_server = | dl = | dl_url = https://github.com/GMOD/GBrowse | dl_src = | dl_src_url = | dl_dev = | dl_dev_url = https://github.com/GMOD/GBrowse | 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 multiple sequence alignments.

More information on GBrowse_syn configuration | doc = 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. | papers = Please refer to the following paper when citing GBrowse_syn:

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

| presentations = * Challenges in Comparative Genome Browsing - Presented by Sheldon McKay at the European Bioinformatics Institute, Hinxton, UK.

| tutorials =

GBrowse_syn_Tutorial
Installing and configuring GBrowse_syn

| wild_urls = *The Arabidopsis Information Resource

| 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. | dev_ppl = | dev_status = See the discussion page for notes on further GBrowse_syn development. | contact_email = Sheldon Mckay | input = | output = | 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:

| demo_server = http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000 | survey_link = GBrowse_syn }}
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