Difference between revisions of "GBrowse Plugins"
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| − | + | Plugins extend GBrowse | |
| − | + | ||
| − | + | For details on how to configure plugins, see [[GBrowse_Configuration_HOWTO#Plugin_Options]]. | |
| − | + | ||
| − | + | Below is an annotated list of GBrowse plugins with pointers to more detailed documentation, where available. Developers, see: [[Creating GBrowse Plugins]]. | |
| − | + | ||
| − | + | ; [[AlignTwoSequences.pm]] : BLASTs an input sequence against the current display, with hits as new sequence features. | |
| − | + | ; [[Aligner.pm]] : Prints out a multiple alignment of the selected features. | |
| − | + | ; [[AttributeHiliter.pm]] : Highlights features whose properties match certain criteria. | |
| − | + | ; [[BatchDumper.pm]] : Dumps out the currently displayed genomic segment or the segments corresponding to the given accessions, in the requested format. | |
| − | + | ; [[Blat.pm]] : Blats an input against the genome of the current organism. | |
| − | + | ; [[CMapDumper.pm]] : Dumps a tab delimited file that can be read by CMap. | |
| − | + | ; [[CreateBlastDB.pm]] : Creates a Blast-formatted database from a Bio::DB::GFF database | |
| − | + | ; [[FastaDumper.pm]] : Dumps out the currently displayed genomic segment in decorated FASTA format. | |
| − | + | ; [[FilterTest.pm]] : Filters the features. | |
| − | + | ; [[GeneFinder.pm]] : A front end to Phil Green's GeneFinder program. | |
| − | + | ; [[GFFDumper.pm]] : Dumps various versions of [[GFF]]. | |
| − | + | ; [[LDAPAuthenticate.pm]] : Authentication via LDAP. | |
| − | + | ; [[MotifFinder.pm]] : Finds sequence specific motifs using Position Frequency Matrix. | |
| − | + | ; [[OligoFinder.pm]] : Finds oligos between 11 and 50 bp in length. | |
| − | + | ; [[Gbrowse/authentication_plugins/PamAuthenticate | PamAuthenticate.pm]] : Authenticate users using Pluggable Authentication Modules. | |
| − | + | ; [[ProteinDumper.pm]] : Dumps translated protein sequences in various formats. | |
| − | + | ; [[PrimerDesigner.pm]] : Real-time design PCR primers for a selected region. | |
| + | ; [[RandomGene.pm]] : Generates random genes, designed to demonstrate annotator plugins. | ||
| + | ; [[RestrictionAnnotator.pm]] : Generates a restriction map on the current view. | ||
| + | ; [[SequenceDumper.pm]] : Dumps sequences I guess. | ||
| + | ; [[Spectrogram.pm]] : Digital signal processing of DNA sequences. | ||
| + | ; [[Submitter.pm]] : Submit selected sequences to external web sites | ||
| + | ; [[TrackFinder.pm]] : Filter and highlight the track listing according to keywords | ||
| + | ; [[gbrowse/authentication_plugins/testauthenticator | TestAuthenticator.pm]] : A simple test of the authentication plugin system that looks for a hardcoded username/password. | ||
| + | ; [[test.pm]] : Used to test that the dump architecture is working properly. | ||
| + | ; YourPlugin.pm : Your cool plugin described here... | ||
[[Category:GBrowse]] | [[Category:GBrowse]] | ||
| + | [[Category:GBrowse Plugins]] | ||
Latest revision as of 17:00, 4 December 2012
Plugins extend GBrowse
For details on how to configure plugins, see GBrowse_Configuration_HOWTO#Plugin_Options.
Below is an annotated list of GBrowse plugins with pointers to more detailed documentation, where available. Developers, see: Creating GBrowse Plugins.
- AlignTwoSequences.pm
- BLASTs an input sequence against the current display, with hits as new sequence features.
- Aligner.pm
- Prints out a multiple alignment of the selected features.
- AttributeHiliter.pm
- Highlights features whose properties match certain criteria.
- BatchDumper.pm
- Dumps out the currently displayed genomic segment or the segments corresponding to the given accessions, in the requested format.
- Blat.pm
- Blats an input against the genome of the current organism.
- CMapDumper.pm
- Dumps a tab delimited file that can be read by CMap.
- CreateBlastDB.pm
- Creates a Blast-formatted database from a Bio::DB::GFF database
- FastaDumper.pm
- Dumps out the currently displayed genomic segment in decorated FASTA format.
- FilterTest.pm
- Filters the features.
- GeneFinder.pm
- A front end to Phil Green's GeneFinder program.
- GFFDumper.pm
- Dumps various versions of GFF.
- LDAPAuthenticate.pm
- Authentication via LDAP.
- MotifFinder.pm
- Finds sequence specific motifs using Position Frequency Matrix.
- OligoFinder.pm
- Finds oligos between 11 and 50 bp in length.
- PamAuthenticate.pm
- Authenticate users using Pluggable Authentication Modules.
- ProteinDumper.pm
- Dumps translated protein sequences in various formats.
- PrimerDesigner.pm
- Real-time design PCR primers for a selected region.
- RandomGene.pm
- Generates random genes, designed to demonstrate annotator plugins.
- RestrictionAnnotator.pm
- Generates a restriction map on the current view.
- SequenceDumper.pm
- Dumps sequences I guess.
- Spectrogram.pm
- Digital signal processing of DNA sequences.
- Submitter.pm
- Submit selected sequences to external web sites
- TrackFinder.pm
- Filter and highlight the track listing according to keywords
- TestAuthenticator.pm
- A simple test of the authentication plugin system that looks for a hardcoded username/password.
- test.pm
- Used to test that the dump architecture is working properly.
- YourPlugin.pm
- Your cool plugin described here...
