Difference between revisions of "GBrowse Plugins"

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Plugins extend GBrowse
An annotated list of GBrowse plugins with pointers to more detailed documentation, where available. See: [[creating plugins]].
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For details on how to configure plugins, see [[GBrowse_Configuration_HOWTO#Plugin_Options]].
  
*'''AlignTwoSequences.pm''' BLASTs an input sequence against the current display, with hits as new sequence features.
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Below is an annotated list of GBrowse plugins with pointers to more detailed documentation, where available. Developers, see: [[Creating GBrowse Plugins]].
*'''Aligner.pm''' prints out a multiple alignment of the selected features.
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*'''AttributeHiliter''' highlights features whose properties match certain criteria.
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; [[AlignTwoSequences.pm]] : BLASTs an input sequence against the current display, with hits as new sequence features.
*'''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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; [[Aligner.pm]] : Prints out a multiple alignment of the selected features.
*'''Blat.pm''' BLATs an input against the genome of the current organism.
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; [[AttributeHiliter.pm]] : Highlights features whose properties match certain criteria.
*'''CMapDumper.pm''' dumps a tab delimited file that can be read by CMap.
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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.
*'''CreateBlastDB.pm''' creates a Blast-formatted database from a Bio::DB::GFF database
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; [[Blat.pm]] : Blats an input against the genome of the current organism.
*'''FastaDumper.pm''' dumps out the currently displayed genomic segment in decorated FASTA format.
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; [[CMapDumper.pm]] : Dumps a tab delimited file that can be read by CMap.
*'''FilterTest.pm''' filters the features.
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; [[CreateBlastDB.pm]] : Creates a Blast-formatted database from a Bio::DB::GFF database
*'''GeneFinder.pm''' a front end to Phil Green's GeneFinder program.
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; [[FastaDumper.pm]] : Dumps out the currently displayed genomic segment in decorated FASTA format.
*'''GFFDumper.pm''' dumps various versions of [[GFF]].
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; [[FilterTest.pm]] : Filters the features.
*'''[[MotifFinder.pm]]''' finds sequence specific motifs using Position Frequency Matrix.
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; [[GeneFinder.pm]] : A front end to Phil Green's GeneFinder program.
*'''OligoFinder.pm''' finds oligos between 11 and 50 bp in length.
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; [[GFFDumper.pm]] : Dumps various versions of [[GFF]].
*'''ProteinDumper''' dumps translated protein sequences in various formats.
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; [[LDAPAuthenticate.pm]] : Authentication via LDAP.
*'''[[PrimerDesigner.pm]]''' real-time design PCR primers for a selected region.
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; [[MotifFinder.pm]] : Finds sequence specific motifs using Position Frequency Matrix.
*'''RandomGene.pm''' generates random genes, designed to demonstrate annotator plugins.
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; [[OligoFinder.pm]] : Finds oligos between 11 and 50 bp in length.
*'''RestrictionAnnotator''' generates a restriction map on the current view.
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; [[Gbrowse/authentication_plugins/PamAuthenticate | PamAuthenticate.pm]] : Authenticate users using Pluggable Authentication Modules.
*'''[[Spectrogram.pm]]''' digital signal processing of DNA sequences.
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; [[ProteinDumper.pm]] : Dumps translated protein sequences in various formats.
*'''[[Submitter.pm]]''' submit selected sequences to external web sites
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; [[PrimerDesigner.pm]] : Real-time design PCR primers for a selected region.
*'''test.pm''' used to test that the dump architecture is working properly.
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; [[RandomGene.pm]] : Generates random genes, designed to demonstrate annotator plugins.
*'''[[Creating plugins|YourPlugin.pm]]''' your cool plugin described here...
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; [[RestrictionAnnotator.pm]] : Generates a restriction map on the current view.
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; [[SequenceDumper.pm]] : Dumps sequences I guess.
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; [[Spectrogram.pm]] : Digital signal processing of DNA sequences.
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; [[Submitter.pm]] : Submit selected sequences to external web sites
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; [[TrackFinder.pm]] : Filter and highlight the track listing according to keywords
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; [[gbrowse/authentication_plugins/testauthenticator | TestAuthenticator.pm]] : A simple test of the authentication plugin system that looks for a hardcoded username/password.
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; [[test.pm]] : Used to test that the dump architecture is working properly.
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; YourPlugin.pm : Your cool plugin described here...
  
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]
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[[Category:GBrowse Plugins]]

Latest revision as of 17:00, 4 December 2012

Plugins extend GBrowse

For details on how to configure plugins, see GBrowse_Configuration_HOWTO#Plugin_Options.

Below is an annotated list of GBrowse plugins with pointers to more detailed documentation, where available. Developers, 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.
LDAPAuthenticate.pm 
Authentication via LDAP.
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.
SequenceDumper.pm 
Dumps sequences I guess.
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...