| This Release | GBrowse-1.9971 | [Download] [Browse] | 19 Aug 2009 | ||||
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| Links | [ Discussion Forum ] [ View/Report Bugs (1) ] [ Dependencies ] [ Other Tools ] | ||||||
| CPAN Testers | PASS (20) FAIL (6) UNKNOWN (2) [ View Reports ] [ Perl/Platform Version Matrix ] | ||||||
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| License | Perl (Artistic and GPL) | ||||||
| Special Files |
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| Bio::DB::GFF::Aggregator::match_gap | GFF3 match aggregator | ||
| Bio::DB::GFF::Aggregator::reftranscript | Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts | 0.10 | |
| Bio::DB::GFF::Aggregator::waba_alignment | A WABA alignment | 0.20 | |
| Bio::DB::GFF::Aggregator::wormbase_gene | Wormbase gene aggregator | 0.30 | |
| Bio::DB::GFF::SyntenyBlock | |||
| Bio::DB::GFF::SyntenyIO | |||
| Bio::DB::Tagger::Iterator | Simple object tagging system | ||
| Bio::DB::Tagger::Tag | Authored tags | ||
| Bio::DB::Tagger::mysql | |||
| Bio::Graphics::Browser | 1.9971 | ||
| Bio::Graphics::Browser::AuthorizedFeatureFile | Add HTTP authorization features to FeatureFile | ||
| Bio::Graphics::Browser::CAlign | Compiled helper for Bio::Graphics::Browser::Realign | ||
| Bio::Graphics::Browser::CachedTrack | |||
| Bio::Graphics::Browser::DataBase | A simple cache for database handles | ||
| Bio::Graphics::Browser::DataSource | |||
| Bio::Graphics::Browser::GFFPrinter | |||
| Bio::Graphics::Browser::GFFhelper | Helps gbrowse plugins handle GFF | ||
| Bio::Graphics::Browser::I18n | |||
| Bio::Graphics::Browser::Markup | Markup routines for sequences in text form | ||
| Bio::Graphics::Browser::MetaSegment | Search through multiple databases for feature matches. | ||
| Bio::Graphics::Browser::OptionPick | Pick options | ||
| Bio::Graphics::Browser::PadAlignment | Insert pads into a multiple alignment | ||
| Bio::Graphics::Browser::Plugin | Base class for gbrowse plugins. | 0.20 | |
| Bio::Graphics::Browser::Plugin::AlignTwoSequences | a plugin that executes NCBI's bl2seq on the current view | 0.02 | |
| Bio::Graphics::Browser::Plugin::Aligner | Dump multiple alignments from GBrowse | 0.23 | |
| Bio::Graphics::Browser::Plugin::AttributeHiliter | hilite features based on attributes | 0.01 | |
| Bio::Graphics::Browser::Plugin::BatchDumper | 1 | ||
| Bio::Graphics::Browser::Plugin::Blat | plugin to map sequences against the genome | 0.01 | |
| Bio::Graphics::Browser::Plugin::CMapDumper | 0.80 | ||
| Bio::Graphics::Browser::Plugin::CreateBlastDB | a plugin that creates a Blast-formatted database from a Bio::DB::GFF database | 0.15 | |
| Bio::Graphics::Browser::Plugin::FBTableDumper | 0.80 | ||
| Bio::Graphics::Browser::Plugin::FastaDumper | 0.20 | ||
| Bio::Graphics::Browser::Plugin::FilterTest | 0.O1 | ||
| Bio::Graphics::Browser::Plugin::GeneFinder | 0.2 | ||
| Bio::Graphics::Browser::Plugin::OligoFinder | 0.15 | ||
| Bio::Graphics::Browser::Plugin::PrimerDesigner | a plugin to design PCR primers with primer3 | ||
| Bio::Graphics::Browser::Plugin::ProteinDumper | A plugin for dumping translated protein sequences in various formats | 1.00 | |
| Bio::Graphics::Browser::Plugin::RandomGene | 0.3 | ||
| Bio::Graphics::Browser::Plugin::RestrictionAnnotator | Generate a restriction map track in GBrowse | 0.25 | |
| Bio::Graphics::Browser::Plugin::SequenceDumper | A plugin for dumping sequences in various formats | 0.12 | |
| Bio::Graphics::Browser::Plugin::SimpleTrackFinder | Limit list of tracks to those that match a name pattern | 0.25 | |
| Bio::Graphics::Browser::Plugin::SinWave | 0.1 | ||
| Bio::Graphics::Browser::Plugin::SourceTrackFinder | Limit list of tracks to those that contain arbitrary fields | 0.25 | |
| Bio::Graphics::Browser::Plugin::Spectrogram | 1.1 | ||
| Bio::Graphics::Browser::Plugin::Submitter | 0.1 | ||
| Bio::Graphics::Browser::Plugin::TestFinder | |||
| Bio::Graphics::Browser::Plugin::TrackDumper | 0.90 | ||
| Bio::Graphics::Browser::Plugin::test | 0.10 | ||
| Bio::Graphics::Browser::PluginSet | A set of plugins | ||
| Bio::Graphics::Browser::Realign | Perl extension for Smith-Waterman alignments | ||
| Bio::Graphics::Browser::Region | |||
| Bio::Graphics::Browser::RemoteSet | A set of plugins | ||
| Bio::Graphics::Browser::Render | |||
| Bio::Graphics::Browser::Render::HTML | |||
| Bio::Graphics::Browser::Render::Slave | |||
| Bio::Graphics::Browser::Render::Slave::Status | |||
| Bio::Graphics::Browser::RenderPanels | |||
| Bio::Graphics::Browser::Session | |||
| Bio::Graphics::Browser::Shellwords | |||
| Bio::Graphics::Browser::UploadSet | A set of uploaded feature files | ||
| Bio::Graphics::Browser::UserData | |||
| Bio::Graphics::Browser::UserTracks | |||
| Bio::Graphics::Browser::Util | Exported utilities | ||
| Bio::Graphics::GBrowseFeature | |||
| Bio::Graphics::Karyotype | |||
| CGI::Toggle | Utility methods for collapsible sections | ||
| GBrowseGuessDirectories | |||
| GBrowseInstall | |||
| InstallUtil | |||
| MobyServices::GbrowseServices | |||
| MobyServices::b64_encoded_gif_renderer | a renderer (HTML) for b64_encoded_gif type MOBY Objects | ||
| MobyServices::b64_encoded_jpeg_renderer | a renderer (HTML) for b64_encoded_jpeg type MOBY Objects | ||
| MobyServices::text_formatted_renderer | a renderer (HTML) for text-formatted type MOBY Objects | ||
| MobyServices::text_html_renderer | a renderer (HTML) for text_html type MOBY Objects | ||
| MobyServices::text_plain_renderer | a renderer (HTML) for text_plain type MOBY Objects | ||
| MobyServices::text_xml_renderer | a renderer (HTML) for text_xml type MOBY Objects |
| Bio::DB::Tagger | Simple object tagging system |
| Bio::Graphics::Browser::RegionSearch | Search through multiple databases for feature matches. |
| auto_install_databases.pl | Download and install GFF data sets |
| bp_load_gff.pl | Load a Bio::DB::GFF database from GFF files. |
| cgi-bin/gbrowse_gmap | |
| docs/pod/BIOSQL_ADAPTER_HOWTO.pod | |
| docs/pod/CONFIGURE_HOWTO.pod | |
| docs/pod/CONTROLLER.pod | |
| docs/pod/DAS_HOWTO.pod | |
| docs/pod/FAQ.pod | |
| docs/pod/GBROWSE_IMG.pod | |
| docs/pod/GENBANK_HOWTO.pod | |
| docs/pod/INSTALL.MacOSX.pod | |
| docs/pod/INSTALL.pod | |
| docs/pod/MAKE_IMAGES_HOWTO.pod | |
| docs/pod/ORACLE_AND_POSTGRESQL.pod | |
| docs/pod/README-berkeley-gadfly.pod | |
| docs/pod/README-chado.pod | |
| docs/pod/README-gff-files.pod | |
| docs/pod/README-lucegene.pod | |
| gbrowse_clean.pl | Clean up sessions and other temporary gbrowse2 files |
| gbrowse_netinstall.pl | |
| load_genbank.pl | Load a Bio::DB::GFF database from GENBANK files. |
| make_das_conf.pl | Create GBrowse config files from DAS sources |
| ncbi_2_gff.pl | Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF |
| package | Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts |
| process_gadfly.pl | Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser |
| process_sgd.pl | Massage SGD annotation flat files into a version suitable for the Generic Genome Browser |
| process_wormbase.pl | Massage WormBase GFF files into a version suitable for the Generic Genome Browser |
| ucsc_genes2gff.pl | Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse |
| wiggle2gff3.pl |
