Difference between revisions of "GBrowse syn"
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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] | ||
| − | =Documentation= | + | =GBrowse_syn Documentation= |
{{SummerSchoolBoxBoth|Gbrowse_syn}} | {{SummerSchoolBoxBoth|Gbrowse_syn}} | ||
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*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 either with the [[GBrowse_Install_HOWTO#The_NetInstaller|GBrowse netinstall script]] (use the -d option) or with a [[GBrowse_Install_HOWTO|source code installation]]. | + | *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]]. |
==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...]]. |
==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 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 | + | * The species' databases are configured in the same way as a regular GBrowse installations |
| − | * | + | * [[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. | ||
* 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. |
| + | * [[GBrowse_syn_Help|Details...]] | ||
==Presentations and Workshops== | ==Presentations and Workshops== | ||
| − | + | * [[:Media:GBrowse_syn_EBI2009.pdf]]|Challenges in Comparative Genome Browsing]] - Presented by [[User:Mckays|Sheldon McKay]] at the European Bioinformatics Institute. | |
| − | * [[: | + | * [[: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 PAG 2009 Workshop]] | ||
* [[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]]. | ||
Revision as of 10:13, 5 August 2009
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.
Contents
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
GBrowse_syn Documentation
There is a session
on Gbrowse_syn at
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 CVS.
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...
Presentations and Workshops
- Media:GBrowse_syn_EBI2009.pdf|Challenges in Comparative Genome Browsing]] - Presented by Sheldon McKay at the European Bioinformatics Institute.
- Comparative Genomics with GBrowse_syn - Presentation by Sheldon McKay at the SMBE 2009 GMOD Workshop on using GBrowse_syn for comparative genomics.
- GBrowse_syn PAG 2009 Workshop
- November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.
