Changes for version 2.15
- Set the "DNA accessor" for databases to the default database. Assuming that the backend supports the dna_accessor() method and that the default database has access to the underlying sequence, then this will enable glyphs and plugins to access the DNA for all features, even if the feature is contained in a database that does not have access to the DNA.
- You can now override the "buttons" images path in individual datasource files.
- You can now have an annotator plugin turned on by default by specifying it in the "default features" option using the syntax "plugin:RestrictionAnnotator".
- Renderfarm slaves now honor the init_code directive. You will need Bio::Graphics version 2.13 in order to take advantage of this feature.
- Added a description of the BED file format to the upload help page.
- Fixed various problems in the ProteinDumper plugin.
- Fixed problems with all regular expression tracks being cached to same directory.
- Fixed issues with uploaded tracks not being displayed when renderfarm activated.
- Fixed issues involving failure of render slaves to preload databases (slowing everything down).
- Fixed incorrect sequence dumping in the sequence dumper when using the Bio::DB::GFF database backend.
- Fixed problems with losing all default tracks when first loading the browser (this was a bug introduced in SVN and never released.)
Documentation
Download and install GFF data sets
Load a Bio::DB::GFF database from GFF files.
Clean up sessions and other temporary gbrowse2 files
Load a Bio::DB::GFF database from GENBANK files.
Create GBrowse config files from DAS sources
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
Massage WormBase GFF files into a version suitable for the Generic Genome Browser
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
convert AXT pairwise alignment files to GFF, Fasta and wig files
convert a phrap produced, ace file into a gff formatted file
Convert a BLAST result file into a GFF file
make gff files from NCBI Map Viewer data files.
Base class for gbrowse plugins.
Modules
a renderer (HTML) for b64_encoded_gif type MOBY Objects
a renderer (HTML) for b64_encoded_jpeg type MOBY Objects
a renderer (HTML) for text-formatted type MOBY Objects
a renderer (HTML) for text_html type MOBY Objects
a renderer (HTML) for text_plain type MOBY Objects
a renderer (HTML) for text_xml type MOBY Objects
a plugin that executes NCBI's bl2seq on the current view
Dump multiple alignments from GBrowse
hilite features based on attributes
plugin to map sequences against the genome
a plugin that creates a Blast-formatted database from a Bio::DB::GFF database
a plugin to design PCR primers with primer3
A plugin for dumping translated protein sequences in various formats
Generate a restriction map track in GBrowse
A plugin for dumping sequences in various formats
Limit list of tracks to those that match a name pattern
Limit list of tracks to those that contain arbitrary fields
Limit list of tracks to those that mention keywords
DAS-style accession to a gus database
DAS-style access to a GUS database
A simple XML sql parser
GFF3 match aggregator
A WABA alignment
Wormbase gene aggregator
Simple object tagging system
Authored tags
Add HTTP authorization features to FeatureFile
Compiled helper for Bio::Graphics::Browser::Realign
A simple cache for database handles
Helps gbrowse plugins handle GFF
Markup routines for sequences in text form
Pick options
Insert pads into a multiple alignment
Base class for gbrowse plugins.
A set of plugins
Perl extension for Smith-Waterman alignments
Search through multiple databases for feature matches.
A set of plugins
Exported utilities
Utility methods for collapsible sections
Compiled helper for Bio::Graphics::Browser::Realign
Provides
in lib/Bio/DB/SeqFeature/Store/BedLoader.pm
in lib/Bio/DB/Tagger.pm
in lib/Bio/DB/Tagger/mysql.pm
in lib/Bio/Graphics/Browser2.pm
in lib/Bio/Graphics/Browser2/Action.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/Browser2/CachedTrack.pm
in lib/Bio/Graphics/Browser2/DataLoader.pm
in lib/Bio/Graphics/Browser2/DataLoader/bam.pm
in lib/Bio/Graphics/Browser2/DataLoader/bed.pm
in lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
in lib/Bio/Graphics/Browser2/DataLoader/generic.pm
in lib/Bio/Graphics/Browser2/DataLoader/gff.pm
in lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
in lib/Bio/Graphics/Browser2/DataLoader/sam.pm
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
in lib/Bio/Graphics/Browser2/DataSource.pm
in lib/Bio/Graphics/Browser2/ExternalData.pm
in lib/Bio/Graphics/Browser2/I18n.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/Region.pm
in lib/Bio/Graphics/Browser2/Render.pm
in lib/Bio/Graphics/Browser2/Render/HTML.pm
in lib/Bio/Graphics/Browser2/Render/Slave.pm
in lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
in lib/Bio/Graphics/Browser2/RenderPanels.pm
in lib/Bio/Graphics/Browser2/Session.pm
in lib/Bio/Graphics/Browser2/Shellwords.pm
in lib/Bio/Graphics/Browser2/SubtrackTable.pm
in lib/Bio/Graphics/Browser2/TrackDumper.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/GBrowseFeature.pm
in lib/Bio/Graphics/Karyotype.pm
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
in lib/Bio/Graphics/Browser2/GFFhelper.pm
in lib/Bio/Graphics/Browser2/DataBase.pm
in lib/Legacy/DB/SyntenyBlock.pm
in lib/Legacy/DB/SyntenyIO.pm
in lib/Legacy/Graphics/Browser.pm
in lib/Legacy/Graphics/Browser/I18n.pm
in lib/Legacy/Graphics/Browser/PageSettings.pm
in lib/Legacy/Graphics/Browser/Synteny.pm
in lib/Legacy/Graphics/Browser/Util.pm
in lib/Legacy/Graphics/Browser.pm
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm