Difference between revisions of "GBrowse syn"

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{{Tool data
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|name=GBrowse_syn
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|full name=Generic Synteny Browser
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|status=beta release
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|dev=active
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|support=active
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|type=Comparative genome visualization
 +
|platform=web
 +
|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).
 +
|open source=Yes
 +
|language=Perl
 +
|release date=2007/01/01
 +
|logo=GBrowse_syn_logo.png
 +
|screenshot=[[Image:GBrowse_syn.png|thumb|none|500px|GBrowse_syn, as implemented at WormBase]]
 +
|mail=Support is via the GBrowse mailing list:{{MailingListsFor|GBrowse}}
 +
|papers=Please refer to the following paper when citing GBrowse_syn:
 +
* 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.
 +
* [[: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]].
 +
|tutorials=;[[GBrowse syn Tutorial]]
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:Installing and configuring GBrowse_syn; from the [[2013 GMOD Summer School]]
 +
|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]].
 +
|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|GBrowse_syn configuration]]
[[File:GBrowse_syn_logo.png|center|400px|alt=GBrowse_syn logo]]
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|doc=See the [[GBrowse_syn_Help|help for GBrowse_syn]]
 
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<div class="componentBox">
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<div class="compBoxHdr">Status</div>
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*Mature release
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*maintenance
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*active support
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<div class="compBoxHdr">Resources</div>
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*[http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ Download]
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*{{2008SurveyLink|#GBrowse_syn|2008 Survey}}
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*[[GBrowse_syn Tutorial]]
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</div>
+
 
+
==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).
+
 
+
 
+
===Screenshots===
+
 
+
[[Image:GBrowse_syn.png|none|400px|GBrowse_syn, as implemented at WormBase]]
+
 
+
==Downloads==
+
 
+
Download GBrowse_syn: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ 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.
+
 
+
==Using GBrowse_syn==
+
 
+
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]].
+
 
+
===Documentation===
+
 
+
See the [[GBrowse_syn_Help|help for GBrowse_syn]]
+
  
 
====Alignment data====
 
====Alignment data====
Line 50: Line 40:
  
 
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.
 +
|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].
 +
|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]
 +
|extra={{GitcComponent}}
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|gmod date=
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|survey link=GBrowse_syn
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|contact email=[mailto:mckays@cshl.edu Sheldon Mckay]
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|integration=
 +
|dev status=See the [[{{TALKPAGENAME}}|discussion page]] for notes on further GBrowse_syn development.
 +
}}
 +
<!-- to alter this page, please edit the raw data, which is stored at http://gmod.org/wiki/GBrowse_syn/tool_data -->
  
==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) <ref name=PMID:20836076/>
 
  
===Tutorials===
 
  
*[[GBrowse_syn_Tutorial|Installing and configuring GBrowse_syn]]
 
 
===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.
 
* [[: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]].
 
 
==Contacts and Mailing Lists==
 
 
Support is via the GBrowse mailing list:
 
 
{| class="wikitable"
 
|
 
! Mailing List Link
 
! Description
 
! Archive(s)
 
|-
 
! rowspan="2" | [[GBrowse]] & [[GBrowse_syn]]
 
| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse gmod-gbrowse]
 
| [[GBrowse]] and [[GBrowse_syn]] users and developers.
 
| [http://dir.gmane.org/gmane.science.biology.gmod.gbrowse Gmane], [http://gmod.827538.n3.nabble.com/GBrowse-f815907.html Nabble (2010/05+)], [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse Sourceforge]
 
|-
 
| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-cmts gmod-gbrowse-cmts]
 
| Code updates.
 
| [http://sourceforge.net/mailarchive/forum.php?forum_name=gmod-gbrowse-cmts Sourceforge]
 
|}
 
 
 
==GBrowse_syn in the wild==
 
 
Public installations of GBrowse_syn:
 
*[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]
 
 
==GBrowse_syn Development==
 
 
 
See the [[Talk:GBrowse_syn|discussion page]] for notes on further GBrowse_syn development.
 
 
 
==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]
 
  
==More on GBrowse_syn==
 
  
See [[:Category:GBrowse_syn]]
 
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].
 
  
  
<references />
+
{{ :GBrowse_syn/tool_data | template = Template:ToolDisplay }}
  
 
[[Category:GBrowse syn]]
 
[[Category:GBrowse syn]]
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[[Category:Comparative Genomics]]
 
[[Category:Comparative Genomics]]
 
[[Category:WormBase]]
 
[[Category:WormBase]]
 +
{{SemanticLink
 +
|linkurl=https://github.com/GMOD/GBrowse
 +
|linktype=download
 +
}}
 +
{{SemanticLink
 +
|linkurl=https://github.com/GMOD/GBrowse
 +
|linktype=source code
 +
}}
 +
{{SemanticLink
 +
|linkurl=http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000
 +
|linktype=demo server
 +
}}
 +
{{SemanticLink
 +
|linkurl=http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501
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|linktitle=The Arabidopsis Information Resource
 +
|linktype=wild URL
 +
}}
 +
{{SemanticLink
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|linkurl=http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000
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|linktitle=WormBase
 +
|linktype=wild URL
 +
}}
 +
{{SemanticLink
 +
|linkurl=http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/
 +
|linktitle=Sol Genomics
 +
|linktype=wild URL
 +
}}

Latest revision as of 21:39, 15 October 2013

GBrowse_syn logo
Status
  • Beta release
  • Development: active
  • Support: active
Resources

Included in

Cloud component

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).


Screenshots

GBrowse_syn, as implemented at WormBase

Downloads


  • 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.


Using GBrowse_syn

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.


Configuration

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

Documentation

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.

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) [1]

Tutorials

GBrowse syn Tutorial
Installing and configuring GBrowse_syn; from the 2013 GMOD Summer School

Presentations

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
gmod-gbrowse-cmts Code updates. Sourceforge

GBrowse_syn in the wild

Public installations of GBrowse_syn:

GBrowse_syn Development

Current status

See the discussion page for notes on further GBrowse_syn development.

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:

More on GBrowse_syn

See Category:GBrowse_syn

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.


  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20836076

Raw tool data at GBrowse_syn/tool data

Facts about "GBrowse syn"RDF feed
Available on platformweb +
Has URLhttps://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 descriptionGBrowse_syn, or the Generic Synteny BrowseGBrowse_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 statusactive +
Has download URLhttps://github.com/GMOD/GBrowse +
Has full nameGeneric Synteny Browser +
Has logoGBrowse_syn_logo.png +
Has software maturity statusbeta release +
Has support statusactive +
Has titleThe Arabidopsis Information Resource +, WormBase + and Sol Genomics +
Has topicGBrowse syn +
Is open sourceYes +
Link typedownload +, source code +, demo server + and wild URL +
Release date1 January 2007 +
Tool functionality or classificationComparative genome visualization +
Written in languagePerl +
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/ +