Difference between revisions of "GBrowse"
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| − | The Generic Genome Browser | + | ==Description== |
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| + | The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes. The Web browser has the following features. | ||
* Simultaneous bird's eye and detailed views of the genome. | * Simultaneous bird's eye and detailed views of the genome. | ||
* Scroll, zoom, center. | * Scroll, zoom, center. | ||
* Attach arbitrary URLs to any annotation. | * Attach arbitrary URLs to any annotation. | ||
| − | * Order and appearance of tracks are customizable by | + | * Order and appearance of tracks are customizable by administrator and end-user. |
* Search by annotation ID, name, or comment. | * Search by annotation ID, name, or comment. | ||
| − | * Supports third party annotation using | + | * Supports third party annotation using [http://www.sanger.ac.uk/software/GFF GFF] formats. |
* Settings persist across sessions. | * Settings persist across sessions. | ||
* DNA and GFF dumps. | * DNA and GFF dumps. | ||
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| − | == | + | ==Documentation== |
Scan through [[the tutorial that comes with the package]] to get a quick overview of its features. | Scan through [[the tutorial that comes with the package]] to get a quick overview of its features. | ||
| − | == | + | |
| + | ==Downloads== | ||
Download the source from the [http://sourceforge.net/project/showfiles.php?group_id=27707 SourceForge download page.], or see the [[instructions]]] for information on installing from a binary distribution (most suitable on MS Windows platforms). | Download the source from the [http://sourceforge.net/project/showfiles.php?group_id=27707 SourceForge download page.], or see the [[instructions]]] for information on installing from a binary distribution (most suitable on MS Windows platforms). | ||
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| − | There are many new features in the current development version which have not been released yet. To get the latest | + | === Getting the Latest & Greatest Version by CVS === |
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| + | There are many new features in the current development version which have not been released yet. To get the latest version, please use anonymous CVS. The recommended branch to use is "gbrowse-sessions" which is more stable than HEAD. Here is the recipe: | ||
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% cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login | % cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login | ||
CVS password: <hit return> | CVS password: <hit return> | ||
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You can also browse the GBrowse CVS [http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/ here.] | You can also browse the GBrowse CVS [http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/ here.] | ||
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== About the Database == | == About the Database == | ||
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* Network adaptors -- read annotations from GenBank, UCSC or Ensembl | * Network adaptors -- read annotations from GenBank, UCSC or Ensembl | ||
| − | == | + | ==Contacts== |
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| + | Please report bugs to the SourceForge [http://sourceforge.net/tracker/?func=add&group_id=27707&atid=391291 Bug Tracker]. | ||
| − | + | Please send questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse GBrowse mailing list]. | |
Revision as of 20:12, 11 February 2007
Contents
Description
The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes. The Web browser has the following features.
- Simultaneous bird's eye and detailed views of the genome.
- Scroll, zoom, center.
- Attach arbitrary URLs to any annotation.
- Order and appearance of tracks are customizable by administrator and end-user.
- Search by annotation ID, name, or comment.
- Supports third party annotation using GFF formats.
- Settings persist across sessions.
- DNA and GFF dumps.
Documentation
Scan through the tutorial that comes with the package to get a quick overview of its features.
Downloads
Download the source from the SourceForge download page., or see the instructions] for information on installing from a binary distribution (most suitable on MS Windows platforms).
Getting the Latest & Greatest Version by CVS
There are many new features in the current development version which have not been released yet. To get the latest version, please use anonymous CVS. The recommended branch to use is "gbrowse-sessions" which is more stable than HEAD. Here is the recipe:
% cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login CVS password: <hit return> % cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r gbrowse-session Generic-Genome-Browser
Once you have successfully checked out the Generic-Genome-Browser distribution, you can simply perform a "cvs update" inside the directory to get recent changes.
You can also browse the GBrowse CVS here.
About the Database
GBrowse has a flexible adaptor system for running off various types of database. Standard adaptors include:
- Flat file adaptors (in-memory, indexed) -- put your annotations in a directory and go!
- Relational database adaptors -- Chado, Bio::DB::GFF, BioSQL
- Network adaptors -- read annotations from GenBank, UCSC or Ensembl
Contacts
Please report bugs to the SourceForge Bug Tracker.
Please send questions to the GBrowse mailing list.
