Difference between revisions of "GBrowse syn"

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[[File:GBrowse_syn_logo.png|center|400px|alt=GBrowse_syn logo]]
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|{{ComponentBoxSectionHeader | Events}}
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|{{SchoolBoxItem|GBrowse_syn}}
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{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}
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<div class="componentBox">
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<!-- {{GBrowse_syn_abstract}} -->
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<div class="compBoxHdr">Status</div>
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=The Generic Synteny Browser=
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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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{{ComponentBoxSectionHeader | Events}}
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{{SchoolBoxItem|GBrowse_syn}}
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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).  Working examples can be seen at [http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 TAIR], [http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 WormBase], and [http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ SGN].
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==About Generic Synteny Browser (GBrowse_syn)==
  
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<p>If you use GBrowse_syn in for a publication, please cite:
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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).
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: McKay SJ, Vergara IA and Stajich, J. 2010. "Using the Generic Synteny Browser (Gbrowse_syn)" in Current Protocols in Bioinformatics (Wiley Interscience) doi: 10.1002/0471250953.bi0912s31</p>
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__TOC__
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===Screenshots===
  
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==Notes on Whole Genome Alignment Data==
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[[Image:GBrowse_syn.png|none|400px|GBrowse_syn, as implemented at WormBase]]
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The focus of this documentation is on the GBrowse_syn application.  However, how to generate whole genome alignments, identify orthologous regions, etc, are the subject of considerable interest, so some background reading is listed below:
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*[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies]
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577869/ article on PECAN and ENREDO]
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*[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN]
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*[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline]
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==Installation==
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==Downloads==
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*GBrowse_syn uses much of the same infrastructure as [[GBrowse]], in terms of species databases, configuration files, perl libraries, etc.
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*It comes as part of the GBrowse distribution, version 1.69 and later ([[GBrowse#On-line_documentation|GBrowse installation info...]]).
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*It differs in that databases and configuration for individual species are linked together via a central configuration file and a joining database that contains reciprocal alignments between all species represented in the browser.
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*We recommend using the most up-to-date version of the application (v. 1.7 or later) either with the [[GBrowse_Install_HOWTO#The_NetInstaller|GBrowse netinstall script]] (use the -d option) or with a [[GBrowse_Install_HOWTO|source code installation from SVN]].
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==Configuration==
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Download GBrowse_syn: [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/]
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* Configuration of GBrowse_syn is much the same as for [[GBrowse]], with database and display options controlled by a configuration file
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* GBrowse_syn uses a main configuration file for general options plus an individual configuration for each species represented in the mutliple sequence alignments
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* [[GBrowse_syn_Configuration|Details...]].
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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]].
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 +
===Documentation===
 +
 
 +
See the [[GBrowse_syn_Help|help for GBrowse_syn]]
 +
 
 +
====Alignment data====
  
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==The Alignment data==
 
 
* GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
 
* GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
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* There is an additional '''''GBrowse''''' database for each species represented in the alignments
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* There is an additional GBrowse database for each species represented in the alignments
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* The species' databases are configured in the same way as a regular GBrowse installations
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* 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]]
 
* [[GBrowse_syn_Database|Details on the GBrowse_syn database]]
  
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==User interface==
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====User interface====
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[[Image:GBrowse_syn.png||thumb|400px|GBrowse_syn, as implemented at WormBase]]
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* The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data.
+
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* GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
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* There is no upward limit of the number of species that can be displayed.
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* [[GBrowse_syn_Help|Help for GBrowse_syn]]
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==Support==
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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).
  
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{{MailingListsFor|GBrowse}}
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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.
  
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==Development==
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==Publications, Tutorials, and Presentations==
  
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See the [[{{TALKPAGENAME}}|discussion page]] for notes on developing GBsyn (as it is affectionately abbreviated).
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===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]]
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 +
===Presentations===
  
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==Presentations and 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_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]].
 
* [[: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]].
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* [[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]].
  
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==Logo==
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==Contacts and Mailing Lists==
  
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Support is via the GBrowse mailing list:
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{| class="wikitable"
 +
|
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! Mailing List Link
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! Description
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! Archive(s)
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|-
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! rowspan="2" | [[GBrowse]] & [[GBrowse_syn]]
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| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse gmod-gbrowse]
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| [[GBrowse]] and [[GBrowse_syn]] users and developers.
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| [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]
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|-
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| [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-cmts gmod-gbrowse-cmts]
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| Code updates.
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| [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].
 
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].
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<references />
  
 
[[Category:GBrowse syn]]
 
[[Category:GBrowse syn]]

Revision as of 16:03, 24 August 2012

__NOTITLE__

GBrowse_syn logo
Status
  • Mature release
  • maintenance
  • active support
Resources
Events

2012 GMOD Summer School

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

Download GBrowse_syn: 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 installation instructions for GBrowse.

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

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

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
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