Difference between revisions of "GBrowse Plugins"

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An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. See: [[creating plugins]].
 
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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*'''[[Aligner.pm]]''' prints out a multiple alignment of the selected features.
*'''Aligner.pm''' prints out a multiple alignment of the selected features.
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*'''AttributeHiliter''' highlights features whose properties match certain criteria.
 
*'''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.
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*'''[[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.
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*'''[[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.
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*'''[[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
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*'''[[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.
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*'''[[FastaDumper.pm]]''' dumps out the currently displayed genomic segment in decorated FASTA format.
*'''FilterTest.pm''' filters the features.
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*'''[[FilterTest.pm]]''' filters the features.
*'''GeneFinder.pm''' a front end to Phil Green's GeneFinder program.
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*'''[[GeneFinder.pm]]''' a front end to Phil Green's GeneFinder program.
*'''GFFDumper.pm''' dumps various versions of [[GFF]].
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*'''[[GFFDumper.pm]]''' dumps various versions of [[GFF]].
 
*'''[[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.
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*'''[[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.
 
*'''[[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.
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*'''[[RandomGene.pm]]''' generates random genes, designed to demonstrate annotator plugins.
*'''RestrictionAnnotator''' generates a restriction map on the current view.
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*'''[[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
 
*'''[[Submitter.pm]]''' submit selected sequences to external web sites

Revision as of 09:59, 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...