Difference between revisions of "GBrowse Plugins"
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| − | An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. | + | An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. See: [[creating plugins]]. |
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*'''AlignTwoSequences.pm''' BLASTs an input sequence against the current display, with hits as new sequence features. | *'''AlignTwoSequences.pm''' BLASTs an input sequence against the current display, with hits as new sequence features. | ||
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*'''[[Submitter.pm]]''' submit selected sequences to external web sites | *'''[[Submitter.pm]]''' submit selected sequences to external web sites | ||
*'''test.pm''' used to test that the dump architecture is working properly. | *'''test.pm''' used to test that the dump architecture is working properly. | ||
| − | *'''[[YourPlugin.pm]]''' your cool plugin described here... | + | *'''[[Creating plugins|YourPlugin.pm]]''' your cool plugin described here... |
[[Category:GBrowse]] | [[Category:GBrowse]] | ||
Revision as of 09:57, 8 July 2010
An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. See: creating 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 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.
- MotifFinder.pm finds sequence specific motifs using Position Frequency Matrix.
- 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...
