Revision as of 09:15, 7 August 2009 (view source) Mckays (Talk | contribs) ← Older edit		Revision as of 13:51, 1 July 2011 (view source) Clements (Talk | contribs) m (→‎The Generic Synteny Browser) Newer edit →
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		+	__NOTITLE__
	<!--__NOEDITSECTION__-->		<!--__NOEDITSECTION__-->
		+	=The Generic Synteny Browser=
		+	<div style="font-size: 120%">
		+	{{#icon: GBrowse_syn_logo.png|GBrowse_syn|200|http://gmod.org/wiki/GBrowse_syn#Logo}}{{GBrowse_syn_abstract}}
		+	<p>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</p>
−	[[image:GBrowse_syn1_small.png|right|thumb|300px|GBrowse_syn running on WormBase]]	+	</div>
−	{{GBrowse_syn_abstract}}	+	<br clear=all/>
−		+
−	<font color=red style="font-size:14pt;color:red">New: </font>	+
−	<span class="pops">[GBRowse_syn Tutotial|GBrowse_syn Tutorial]]</span>	+
		+	{{ComponentBox|{{GBrowse_synResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|||{{WCGBoxItem}}| | |}}
		+	__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==	+	=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]].	+	*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
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	* [[GBrowse_syn_Database|Details...]]		* [[GBrowse_syn_Database|Details...]]
−	==User interface==	+	=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==	+	= Support =
		+
		+	{{MailingListsFor|GBrowse}}
		+
		+	= Development =
		+	See the [[{{TALKPAGENAME}}|discussion page]] for notes on developing GBsyn (as it is affectionately abbreviated).
		+
		+	= 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]].
		+
		+	= 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].
	[[Category:GBrowse syn]]		[[Category:GBrowse syn]]

---

Revision as of 13:51, 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

Status

• Mature release
• Active development
• Active support

Resources

• Alignment Primer
• Tutorial
• Configuration
• Help
• Example
• Mailing List
• 2008 Survey
  Events
  
  

Workshop on
Comparative Genomics
July 10-23

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:

• Primer on Hierarchical Genome Alignment Strategies
• article on PECAN and ENREDO
• all about PECAN
• Information about EnsEMBL's compara pipeline

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...

User interface

• 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.
• Details...

Support

Development

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

Presentations and Workshops

• Challenges in Comparative Genome Browsing - Presented by Sheldon McKay at the European Bioinformatics Institute, Hinxton, UK.
• Comparative Genomics with GBrowse_syn - Presentation by Sheldon McKay at the SMBE 2009 GMOD Workshop on using GBrowse_syn for comparative genomics.
• GBrowse_syn at PAG - Presentation by Sheldon McKay at the Plant and Animal Genomes meeting, San Diego, CA, USA.
• November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.

Logo

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.