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