Difference between revisions of "GBrowse syn"
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GBrowse_syn is a synteny browser derived from [[GBrowse]]. It has many of the same zoom, pan and other genome navigation options. It designed as a synteny browser for three or more genomes. A working example can be seen at [http://dev.wormbase.org/db/seq/gbrowse_syn WormBase]. | GBrowse_syn is a synteny browser derived from [[GBrowse]]. It has many of the same zoom, pan and other genome navigation options. It designed as a synteny browser for three or more genomes. A working example can be seen at [http://dev.wormbase.org/db/seq/gbrowse_syn WormBase]. | ||
| − | =Documentation= | + | ==Documentation== |
GBrowse_syn uses the same infrastructure as Gbrowse, in terms of species databases, etc. It differs in that databases and configuration for indivaidual species are linked together via a central configuration file and an alignment database. | GBrowse_syn uses the same infrastructure as Gbrowse, in terms of species databases, etc. It differs in that databases and configuration for indivaidual species are linked together via a central configuration file and an alignment database. | ||
| − | ==Configuration== | + | ===Configuration=== |
| − | ===Configuration files=== | + | ====Configuration files==== |
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. An example from wormbase is shown below. | The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. An example from wormbase is shown below. | ||
<pre> | <pre> | ||
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| − | ===The Alignments database=== | + | ====The Alignments database==== |
| − | ==Examples== | + | ===Examples=== |
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| + | ===Presentations=== | ||
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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]]. | ||
Revision as of 17:34, 27 December 2007
GBrowse_syn is a synteny browser derived from GBrowse. It has many of the same zoom, pan and other genome navigation options. It designed as a synteny browser for three or more genomes. A working example can be seen at WormBase.
Contents
Documentation
GBrowse_syn uses the same infrastructure as Gbrowse, in terms of species databases, etc. It differs in that databases and configuration for indivaidual species are linked together via a central configuration file and an alignment database.
Configuration
Configuration files
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. An example from wormbase is shown below.
The Alignments database
Examples
Presentations
- November 2007 - Sheldon McKay's presentation on GBrowse_syn at the November 2007 GMOD Meeting.
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