Difference between revisions of "GBrowse syn"

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=The Generic Synteny Browser=
 
=The Generic Synteny Browser=
  
[[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).  &nbsp;Working examples can be seen at [http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 TAIR], <span class="pops">[http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 WormBase]</span>, and [http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ SGN].
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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].
  
 
<p>If you use GBrowse_syn in for a publication, please cite:
 
<p>If you use GBrowse_syn in for a publication, please cite:
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__TOC__
 
__TOC__
  
=Notes on Whole Genome Alignment Data=
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==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:
 
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:
*<span class="pops">[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies]</span>
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*[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies]
*<span class="pops">[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2577869 article on PECAN and ENREDO]</span>
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577869/ article on PECAN and ENREDO]
*<span class="pops">[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN]</span>
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*[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN]
*<span class="pops">[http://feb2006.archive.ensembl.org/info/software/compara/index.html Information about EnsEMBL's compara pipeline]
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*[http://www.ensembl.org/info/website/archives/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 [[GBrowse]], 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 SVN]].
 
*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=
+
==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=
+
==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
 
* The species' databases are configured in the same way as a regular GBrowse installations
 
* The species' databases are configured in the same way as a regular GBrowse installations
* [[GBrowse_syn_Database|Details...]]
+
* [[GBrowse_syn_Database|Details on the GBrowse_syn database]]
  
=User interface=
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==User interface==
 
[[Image:GBrowse_syn.png||thumb|400px|GBrowse_syn, as implemented at WormBase]]
 
[[Image:GBrowse_syn.png||thumb|400px|GBrowse_syn, as implemented at WormBase]]
 
* 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
 
* There is no upward limit of the number of species that can be displayed.
 
* There is no upward limit of the number of species that can be displayed.
* [[GBrowse_syn_Help|Details...]]
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* [[GBrowse_syn_Help|Help for GBrowse_syn]]
  
= Support =
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==Support==
  
 
{{MailingListsFor|GBrowse}}
 
{{MailingListsFor|GBrowse}}
  
= Development =
+
==Development==
 +
 
 
See the [[{{TALKPAGENAME}}|discussion page]] for notes on developing GBsyn (as it is affectionately abbreviated).
 
See the [[{{TALKPAGENAME}}|discussion page]] for notes on developing GBsyn (as it is affectionately abbreviated).
  
= Presentations and Workshops =
+
==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]].
  
= Logo =
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==Logo==
  
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].
+
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].
  
 
[[Category:GBrowse syn]]
 
[[Category:GBrowse syn]]

Revision as of 21:32, 8 August 2012

__NOTITLE__

Status
  • Mature release
  • Active development
  • Active support
Resources
Events

2012 GMOD Summer School

{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}

The Generic Synteny Browser

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

  • GBrowse_syn uses much of the same infrastructure as GBrowse, in terms of species databases, configuration files, perl libraries, etc.
  • It comes as part of the GBrowse distribution, version 1.69 and later (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.
  • We recommend using the most up-to-date version of the application (v. 1.7 or later) either with the GBrowse netinstall script (use the -d option) or with a source code installation from SVN.

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 mutliple sequence alignments
  • Details....

The 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 species' databases are configured in the same way as a regular GBrowse installations
  • Details on the GBrowse_syn database

User interface

GBrowse_syn, as implemented at WormBase
  • 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
  • There is no upward limit of the number of species that can be displayed.
  • Help for GBrowse_syn

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.