Difference between revisions of "GBrowse syn"
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{{Tool data | {{Tool data | ||
|name=GBrowse_syn | |name=GBrowse_syn | ||
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|platform=web | |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). | |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 | |
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− | |open source= | + | |
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|language=Perl | |language=Perl | ||
− | | | + | |release date=2007/01/01 |
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|logo=GBrowse_syn_logo.png | |logo=GBrowse_syn_logo.png | ||
|screenshot=[[Image:GBrowse_syn.png|thumb|none|500px|GBrowse_syn, as implemented at WormBase]] | |screenshot=[[Image:GBrowse_syn.png|thumb|none|500px|GBrowse_syn, as implemented at WormBase]] | ||
− | + | |mail=Support is via the GBrowse mailing list:{{MailingListsFor|GBrowse}} | |
− | |mail=Support is via the GBrowse mailing list: | + | |
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− | {{MailingListsFor|GBrowse}} | + | |
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|papers=Please refer to the following paper when citing GBrowse_syn: | |papers=Please refer to the following paper when citing GBrowse_syn: | ||
* Using the Generic Synteny Browser (GBrowse_syn) <ref name=PMID:20836076/> | * Using the Generic Synteny Browser (GBrowse_syn) <ref name=PMID:20836076/> | ||
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:Installing and configuring GBrowse_syn; from the [[2013 GMOD Summer School]] | :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]]. | |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]]. | ||
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|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. | |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. | ||
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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. | 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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|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]. | |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: | |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: | ||
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*[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline] | *[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline] | ||
|extra={{GitcComponent}} | |extra={{GitcComponent}} | ||
+ | |gmod date= | ||
+ | |survey link=GBrowse_syn | ||
+ | |contact email=[mailto:mckays@cshl.edu Sheldon Mckay] | ||
+ | |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 --> | ||
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+ | {{ :GBrowse_syn/tool_data | template = Template:ToolDisplay }} | ||
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+ | [[Category:GBrowse syn]] | ||
+ | [[Category:GMOD Components]] | ||
+ | [[Category:GMOD Developers]] | ||
+ | [[Category:GBrowse]] | ||
+ | [[Category:Comparative Genomics]] | ||
+ | [[Category:WormBase]] | ||
{{SemanticLink | {{SemanticLink | ||
|linkurl=https://github.com/GMOD/GBrowse | |linkurl=https://github.com/GMOD/GBrowse | ||
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|linktype=wild URL | |linktype=wild URL | ||
}} | }} | ||
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Latest revision as of 21:39, 15 October 2013
- Beta release
- Development: active
- Support: active
Included in
Contents
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
Downloads
- Download GBrowse_syn: https://github.com/GMOD/GBrowse
- 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
- 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.
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:
- Primer on Hierarchical Genome Alignment Strategies
- article on PECAN and ENREDO
- all about PECAN
- Information about EnsEMBL's compara pipeline
More on GBrowse_syn
GBrowse_syn 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.
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID:20836076
Raw tool data at GBrowse_syn/tool data
Available on platform | web + |
Has URL | https://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 description | GBrowse_syn, or the Generic Synteny Browse … 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). GBrowse package (version 1.69 and later). + |
Has development status | active + |
Has download URL | https://github.com/GMOD/GBrowse + |
Has full name | Generic Synteny Browser + |
Has logo | GBrowse_syn_logo.png + |
Has software maturity status | beta release + |
Has support status | active + |
Has title | The Arabidopsis Information Resource +, WormBase + and Sol Genomics + |
Has topic | GBrowse syn + |
Is open source | Yes + |
Link type | download +, source code +, demo server + and wild URL + |
Release date | 1 January 2007 + |
Tool functionality or classification | Comparative genome visualization + |
Written in language | Perl + |
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/ + |