Changes for version 2.05
- This will improve performance, but requires Bio::Graphics version 1.05.
- Experimental local rendering code -- each track is rendered in a separate process.
- Reverted to older versions of prototype and scriptaculous due to Google Chrome incompatibilities.
- Preferred way to separate labels is now to use the "l" option and separate labels with "%1E", as in "l=mdc-1%1Esma-23%1Eunknown genes"
- Work around race conditions in the 05.deferredrendering regression tests. May still fail if system is under lots of load during test.
- Fixed bug in change_track_order javascript that prevented track order change from "sticking" when track labels contained underscores.
- Download icons now selectively download GFF3, SAM or WIG data.
- Early support for a "show_summary" option in [TRACK DEFAULTS] and [TRACK] stanzas. If this is present and set to a length in bases, then when the user tries to display a region larger than the length the track will display feature density instead. For this to work, the database adaptor must support a feature_summary() method. This is being actively worked on in bioperl, but is not currently available.
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/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/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