Difference between revisions of "GBrowse syn/tool data"
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| name = GBrowse_syn | | name = GBrowse_syn | ||
| full_name = Generic Synteny Browser | | full_name = Generic Synteny Browser | ||
− | | status = | + | | status = beta release |
− | | dev = | + | | dev = active |
− | | | + | | support = active |
+ | | type = Comparative genome visualization | ||
+ | | platform = web | ||
| logo = GBrowse_syn_logo.png | | logo = GBrowse_syn_logo.png | ||
| home = | | home = | ||
| 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). | ||
− | | screenshot = [[Image:GBrowse_syn.png|none| | + | | screenshot = [[Image:GBrowse_syn.png|thumb|none|500px|GBrowse_syn, as implemented at WormBase]] |
| public_server = | | public_server = | ||
| dl = | | dl = | ||
− | | dl_url = | + | | dl_url = https://github.com/GMOD/GBrowse |
| dl_src = | | dl_src = | ||
| dl_src_url = | | dl_src_url = | ||
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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. | ||
| 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/> | ||
| presentations = * [[: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. | | presentations = * [[: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. | ||
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* [[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]]. | ||
− | | tutorials = | + | | tutorials = |
+ | ;[[GBrowse syn Tutorial]] | ||
+ | :Installing and configuring GBrowse_syn; from the [[2013 GMOD Summer School]] | ||
| wild_urls = *[http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 The Arabidopsis Information Resource] | | wild_urls = *[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://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 WormBase] | ||
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| dev_ppl = | | dev_ppl = | ||
| dev_status = See the [[{{TALKPAGENAME}}|discussion page]] for notes on further GBrowse_syn development. | | dev_status = See the [[{{TALKPAGENAME}}|discussion page]] for notes on further GBrowse_syn development. | ||
− | | contact_email = | + | | contact_email = [mailto:mckays@cshl.edu Sheldon Mckay] |
− | | | + | | input = |
+ | | output = | ||
| 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: | ||
*[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies] | *[http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-104.html Primer on Hierarchical Genome Alignment Strategies] | ||
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*[http://www.ebi.ac.uk/~bjp/pecan/ all about PECAN] | *[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] | *[http://www.ensembl.org/info/website/archives/index.html Information about EnsEMBL's compara pipeline] | ||
− | | demo_server = | + | | demo_server = http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000 |
| survey_link = GBrowse_syn | | survey_link = GBrowse_syn | ||
+ | |release date=2007 | ||
+ | | extras = | ||
+ | {{GitcComponent}} | ||
}} | }} | ||
Latest revision as of 18:33, 10 September 2013
{{ {{{template}}} | name = GBrowse_syn | full_name = Generic Synteny Browser | status = beta release | dev = active | support = active | type = Comparative genome visualization | platform = web | logo = GBrowse_syn_logo.png | home = | 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).
| screenshot =| public_server = | dl = | dl_url = https://github.com/GMOD/GBrowse | dl_src = | dl_src_url = | dl_dev = | dl_dev_url = https://github.com/GMOD/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 installation instructions for GBrowse. | req = | install = | 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.
More information on GBrowse_syn configuration | doc = 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. | papers = Please refer to the following paper when citing GBrowse_syn:
- Using the Generic Synteny Browser (GBrowse_syn) [1]
| 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.
| tutorials =
- GBrowse syn Tutorial
- Installing and configuring GBrowse_syn; from the 2013 GMOD Summer School
| wild_urls = *The Arabidopsis Information Resource
| mail = 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 |
| logo_info = 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. | dev_ppl = | dev_status = See the discussion page for notes on further GBrowse_syn development. | contact_email = Sheldon Mckay | input = | output = | 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
| demo_server = http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000 | survey_link = GBrowse_syn |release date=2007 | extras =
Included in
}}
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