GBrowse Plugins
From GMOD
An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. 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.
- 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.
- 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...