Difference between revisions of "GBrowse Plugins"

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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.
 
 
=Plugin Installation=
 
 
 
=General Plugin Configuration=
 
 
  
 
=Plugins=
 
=Plugins=
*'''[[Submitter.pm]]''' submit selected sequences to external web sites.
+
*'''AlignTwoSequences''' BLASTs an input sequence against the current display, with hits as new sequence features.
*'''[[GFFDumper.pm]]''' dump various versions of [[GFF]].
+
*'''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...