Difference between revisions of "GBrowse Plugins"

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*'''FilterTest.pm''' filters the features.
 
*'''FilterTest.pm''' filters the features.
 
*'''GeneFinder.pm''' a front end to Phil Green's GeneFinder program.
 
*'''GeneFinder.pm''' a front end to Phil Green's GeneFinder program.
*'''[[GFFDumper.pm]]''' dumps various versions of [[GFF]].
+
*'''GFFDumper.pm''' dumps various versions of [[GFF]].
 
*'''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.
 
*'''ProteinDumper''' dumps translated protein sequences in various formats.

Revision as of 19:14, 18 July 2009

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

  • 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.
  • 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...