Difference between revisions of "GBrowse Plugins"
From GMOD
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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. | ||
*'''[[Aligner.pm]]''' prints out a multiple alignment of the selected features. | *'''[[Aligner.pm]]''' prints out a multiple alignment of the selected features. | ||
| − | *'''AttributeHiliter''' highlights features whose properties match certain criteria. | + | *'''[[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. | *'''[[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. | *'''[[Blat.pm]]''' BLATs an input against the genome of the current organism. | ||
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*'''[[MotifFinder.pm]]''' finds sequence specific motifs using Position Frequency Matrix. | *'''[[MotifFinder.pm]]''' finds sequence specific motifs using Position Frequency Matrix. | ||
*'''[[OligoFinder.pm]]''' finds oligos between 11 and 50 bp in length. | *'''[[OligoFinder.pm]]''' finds oligos between 11 and 50 bp in length. | ||
| − | *'''ProteinDumper''' dumps translated protein sequences in various formats. | + | *'''[[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. | *'''[[PrimerDesigner.pm]]''' real-time design PCR primers for a selected region. | ||
*'''[[RandomGene.pm]]''' generates random genes, designed to demonstrate annotator plugins. | *'''[[RandomGene.pm]]''' generates random genes, designed to demonstrate annotator plugins. | ||
| − | *'''RestrictionAnnotator''' generates a restriction map on the current view. | + | *'''[[RestrictionAnnotator.pm]]''' 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 | *'''[[Submitter.pm]]''' submit selected sequences to external web sites | ||
| − | *'''test.pm''' used to test that the dump architecture is working properly. | + | *'''[[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]] | ||
Revision as of 20:48, 18 January 2011
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...
