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GBrowse-1.984
River stage zero No dependents
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Documentation

auto_install_databases.pl
Download and install GFF data sets
bp_load_gff.pl
Load a Bio::DB::GFF database from GFF files.
gbrowse_netinstall.pl
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
process_gadfly.pl
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
ncbi_2_gff.pl
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
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
axt2phy.pl
convert AXT pairwise alignment files to GFF, Fasta and wig files
ace2gff.pl
convert a phrap produced, ace file into a gff formatted file
blast2gff.pl
Convert a BLAST result file into a GFF file
import_ncbi_mv_hs.pl
make gff files from NCBI Map Viewer data files.
contrib::install_macosx::README
pod::BIOSQL_ADAPTER_HOWTO
pod::CONFIGURE_HOWTO
pod::CONTROLLER
pod::DAS_HOWTO
pod::FAQ
pod::GBROWSE_IMG
pod::GENBANK_HOWTO
pod::INSTALL.MacOSX
pod::INSTALL
pod::MAKE_IMAGES_HOWTO
pod::ORACLE_AND_POSTGRESQL
Bio::Graphics::Browser::Plugin
Base class for gbrowse plugins.
pod::README-berkeley-gadfly
pod::README-chado
pod::README-gff-files
pod::README-lucegene

Modules

b64_encoded_gif_renderer.pm
a renderer (HTML) for b64_encoded_gif type MOBY Objects
b64_encoded_jpeg_renderer.pm
a renderer (HTML) for b64_encoded_jpeg type MOBY Objects
text_formatted_renderer.pm
a renderer (HTML) for text-formatted type MOBY Objects
text_html_renderer.pm
a renderer (HTML) for text_html type MOBY Objects
text_plain_renderer.pm
a renderer (HTML) for text_plain type MOBY Objects
text_xml_renderer.pm
a renderer (HTML) for text_xml type MOBY Objects
Bio::Graphics::Browser::Plugin::AlignTwoSequences
a plugin that executes NCBI's bl2seq on the current view
Bio::Graphics::Browser::Plugin::Aligner
Dump multiple alignments from GBrowse
Bio::Graphics::Browser::Plugin::Blat
plugin to map sequences against the genome
Bio::Graphics::Browser::Plugin::CreateBlastDB
a plugin that creates a Blast-formatted database from a Bio::DB::GFF database
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
Bio::Graphics::Browser::Plugin::RestrictionAnnotator
Generate a restriction map track in GBrowse
Bio::Graphics::Browser::Plugin::SequenceDumper
A plugin for dumping sequences in various formats
Bio::Graphics::Browser::Plugin::Spectrogram
contrib/Coverage/plugin/Coverage.pm
DAS::GUS
DAS-style accession to a gus database
DAS::GUS::Segment
DAS-style access to a GUS database
DAS::GUS::Segment::Feature
DAS::Util
A simple XML sql parser
contrib/install_macosx/BuildConfig.pm
install_util/GBrowseInstall.pm
Bio::Graphics::Browser::DataBase
A simple cache for database handles
Bio::Graphics::Browser::GFFhelper
Helps gbrowse plugins handle GFF
Bio::Graphics::Browser::Markup
Markup routines for sequences in text form
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.
Bio::Graphics::Browser::PluginSet
A set of plugins
Bio::Graphics::Browser::Realign
Perl extension for Smith-Waterman alignments
Bio::Graphics::Browser::RegionSearch
Search through multiple databases for feature matches.
Bio::Graphics::Browser::RemoteSet
A set of plugins
Bio::Graphics::Browser::UploadSet
A set of uploaded feature files
Bio::Graphics::Browser::Util
Exported utilities
Bio::Graphics::Browser::CAlign
Compiled helper for Bio::Graphics::Browser::Realign

Provides

Bio::Graphics::Browser
in lib/Bio/Graphics/Browser.pm
Bio::Graphics::Browser::CachedTrack
in lib/Bio/Graphics/Browser/CachedTrack.pm
Bio::Graphics::Browser::DataSource
in lib/Bio/Graphics/Browser/DataSource.pm
Bio::Graphics::Browser::GFFPrinter
in lib/Bio/Graphics/Browser/GFFPrinter.pm
Bio::Graphics::Browser::I18n
in lib/Bio/Graphics/Browser/I18n.pm
Bio::Graphics::Browser::MetaSegment
in lib/Bio/Graphics/Browser/RegionSearch.pm
Bio::Graphics::Browser::MetaSegment::Iterator
in lib/Bio/Graphics/Browser/RegionSearch.pm
Bio::Graphics::Browser::Region
in lib/Bio/Graphics/Browser/Region.pm
Bio::Graphics::Browser::Render
in lib/Bio/Graphics/Browser/Render.pm
Bio::Graphics::Browser::Render::HTML
in lib/Bio/Graphics/Browser/Render/HTML.pm
Bio::Graphics::Browser::Render::Slave
in lib/Bio/Graphics/Browser/Render/Slave.pm
Bio::Graphics::Browser::Render::Slave::Status
in lib/Bio/Graphics/Browser/Render/Slave/Status.pm
Bio::Graphics::Browser::RenderPanels
in lib/Bio/Graphics/Browser/RenderPanels.pm
Bio::Graphics::Browser::Session
in lib/Bio/Graphics/Browser/Session.pm
Bio::Graphics::Browser::Shellwords
in lib/Bio/Graphics/Browser/Shellwords.pm
Bio::Graphics::Browser::UserData
in lib/Bio/Graphics/Browser/UserData.pm
Bio::Graphics::GBrowseFeature
in lib/Bio/Graphics/GBrowseFeature.pm
Bio::Graphics::Karyotype
in lib/Bio/Graphics/Karyotype.pm
FakeHomol
in lib/Bio/Graphics/Browser/GFFhelper.pm

Other files