Difference between revisions of "GBrowse Plugins"
From GMOD
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This is a stub that will be expanded give an annotated list of GBrowse plugins with pointers to more detailed documentation. | This is a stub that will be expanded give an annotated list of GBrowse plugins with pointers to more detailed documentation. | ||
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=Plugins= | =Plugins= | ||
− | *''' | + | *'''AlignTwoSequences''' BLASTs an input sequence against the current display, with hits as new sequence features. |
− | *'''[[GFFDumper.pm]]''' | + | *'''Aligner.pm''' prints out a multiple alignment of the selected features. |
− | *'''[[PrimerDesigner.pm]]''' real-time design PCR primers for a selected region. | + | *'''AttributeHiliter''' 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]]. | ||
+ | *'''OligoFinder.pm''' finds oligos between 11 and 50 bp in length. | ||
+ | *'''ProteinDumper''' 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''' generates a restriction map on the current view. | ||
*'''[[Spectrogram.pm]]''' digital signal processing of DNA sequences. | *'''[[Spectrogram.pm]]''' digital signal processing of DNA sequences. | ||
+ | *'''[[Submitter.pm]]''' submit selected sequences to external web sites | ||
+ | *'''test.pm''' used to test that the dump architecture is working properly. | ||
*'''[[YourPlugin.pm]]''' your cool plugin described here... | *'''[[YourPlugin.pm]]''' your cool plugin described here... |
Revision as of 16:49, 15 January 2008
This is a stub that will be expanded give an annotated list of GBrowse plugins with pointers to more detailed documentation.
Plugins
- AlignTwoSequences 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 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.
- OligoFinder.pm finds oligos between 11 and 50 bp in length.
- ProteinDumper 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 generates a restriction map on the current view.
- Spectrogram.pm digital signal processing of DNA sequences.
- Submitter.pm submit selected sequences to external web sites
- test.pm used to test that the dump architecture is working properly.
- YourPlugin.pm your cool plugin described here...