Difference between revisions of "GBrowse syn"

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=The Generic Synteny Browser=
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<div style="font-size: 120%">
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{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}{{GBrowse_syn_abstract}}
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<p>If you use GBrowse_syn in for a publication, please cite:
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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>
  
[[image:GBrowse_syn1_small.png|right|thumb|300px|GBrowse_syn running on WormBase]]
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</div>
{{GBrowse_syn_abstract}}
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<br clear=all/>
 
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<font color=red style="font-size:14pt;color:red">New: </font>  
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<span class="pops">[GBRowse_syn Tutotial|GBrowse_syn Tutorial]]</span>
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{{ComponentBox|{{GBrowse_synResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|||{{WCGBoxItem}}| | |}}
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__TOC__
  
 
=Notes on Whole Genome Alignment Data=
 
=Notes on Whole Genome Alignment Data=
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*<span class="pops">[http://feb2006.archive.ensembl.org/info/software/compara/index.html Information about EnsEMBL's compara pipeline]
 
*<span class="pops">[http://feb2006.archive.ensembl.org/info/software/compara/index.html Information about EnsEMBL's compara pipeline]
  
==Installation==
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=Installation=
 
*GBrowse_syn uses much of the same infrastructure as <span class=pops>[[GBrowse]]</span>, in terms of species databases, configuration files, perl libraries, etc.
 
*GBrowse_syn uses much of the same infrastructure as <span class=pops>[[GBrowse]]</span>, in terms of species databases, configuration files, perl libraries, etc.
 
*It comes as part of the GBrowse distribution, version 1.69 and later ([[GBrowse#On-line_documentation|GBrowse installation info...]]).
 
*It comes as part of the GBrowse distribution, version 1.69 and later ([[GBrowse#On-line_documentation|GBrowse installation info...]]).
 
*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.
 
*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.
*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 CVS]].
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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]].
  
==Configuration==
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=Configuration=
 
* Configuration of GBrowse_syn is much the same as for [[GBrowse]], with database and display options controlled by a configuration file
 
* 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
 
* GBrowse_syn uses a main configuration file for general options plus an individual configuration for each species represented in the mutliple sequence alignments
 
* [[GBrowse_syn_Configuration|Details...]].
 
* [[GBrowse_syn_Configuration|Details...]].
  
==The 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
 
* There is an additional '''''GBrowse''''' database for each species represented in the alignments
 
* There is an additional '''''GBrowse''''' database for each species represented in the alignments
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* [[GBrowse_syn_Database|Details...]]
 
* [[GBrowse_syn_Database|Details...]]
  
==User interface==
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=User interface=
 
* The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data.
 
* The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data.
 
* GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
 
* GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species
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* [[GBrowse_syn_Help|Details...]]
 
* [[GBrowse_syn_Help|Details...]]
  
==Presentations and Workshops==
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= Support =
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{{MailingListsFor|GBrowse}}
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= Development =
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See the [[{{TALKPAGENAME}}|discussion page]] for notes on developing GBsyn (as it is affectionately abbreviated).
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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]].
 
* [[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]].
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= Logo =
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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.linn-benton.edu Linn-Benton Community College].
  
 
[[Category:GBrowse syn]]
 
[[Category:GBrowse syn]]

Revision as of 17:51, 1 July 2011

__NOTITLE__

The Generic Synteny Browser

{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}
GBrowse_syn, as implemented at WormBase

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 TAIR, WormBase, and SGN.

If you use GBrowse_syn in for a publication, please cite:

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


Notes on Whole Genome Alignment Data

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:

Installation

Configuration

The Alignment data

User interface

Support

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

Development

See the discussion page for notes on developing GBsyn (as it is affectionately abbreviated).

Presentations and Workshops

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.

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