Difference between revisions of "GBrowse Plugins"
From GMOD
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*'''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]]. | ||
+ | *'''[[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. | *'''ProteinDumper''' dumps translated protein sequences in various formats. |
Revision as of 22:33, 5 April 2010
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.
- 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...