Generic Genome Browser
Welcome to the Generic Genome Browser!
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
For future reference, here is where you've installed GBrowse's various
- GBrowse documentation, stylesheets and in-memory databases.
- /usr/local/src/gbrowse (also available for browsing at
- GBrowse configuration files
- GBrowse CGI (web) scripts
- Online tutorial
- /usr/local/src/gbrowse/tutorial (available for browsing at http://localhost/gbrowse/tutorial/tutorial.html).
- Reference manual
- /usr/local/src/gbrowse/docs/pod/INSTALL.html (available for browsing at http://localhost/gbrowse/docs/pod/INSTALL.html).
- /usr/local/src/gbrowse/docs/pod/CONFIGURE_HOWTO.html (available for browsing at http://localhost/gbrowse/docs/pod/CONFIGURE_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/MAKE_IMAGES_HOWTO.html gives directions for creating stand-alone pictures with the gbrowse_img script (at http://localhost/gbrowse/docs/pod/MAKE_IMAGES_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/README-gff-files.html describes methods for obtaining GBrowse compatible GFF files from WormBase, FlyBase, SGD and NCBI/human (at http://localhost/gbrowse/docs/pod/README-gff-files.html).
- /usr/local/src/gbrowse/docs/pod/PLUGINS_HOWTO.html gives directions for creating plugins (at http://localhost/gbrowse/docs/pod/PLUGINS_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/README-chado.html gives notes for using GBrowse with chado (at http://localhost/gbrowse/docs/pod/README-chado.html).
- /usr/local/src/gbrowse/docs/pod/DAS_HOWTO.html gives notes for using GBrowse as a Distributed Annotation System (DAS) server and client (at http://localhost/gbrowse/docs/pod/DAS_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/ORACLE_AND_POSTGRESQL.html gives notes for running GBrowse on top of Oracle and PostgreSQL database servers (at http://localhost/gbrowse/docs/pod/ORACLE_AND_POSTGRESQL.html).
- /usr/local/src/gbrowse/docs/pod/BIOSQL_ADAPTER_HOWTO.html has instructions for running GBrowse on top of a BioSQL database (at http://localhost/gbrowse/docs/pod/BIOSQL_ADAPTER_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/GENBANK_HOWTO.html has notes for loading and browsing GenBank formated files (at http://localhost/gbrowse/docs/pod/GENBANK_HOWTO.html).
- /usr/local/src/gbrowse/docs/pod/INSTALL.MacOSX.html has notes for installing GBrowse on MacOSX (at http://localhost/gbrowse/docs/pod/INSTALL.MacOSX.html).
- Sample data
- Contributed modules and utilities
More Data Sets
To load larger data sets it is suggested that you create a MySQL
database. Sample data from yeast is located in the gbrowse
distribution in the directory sample_data. Instructions for
loading this data is in INSTALL. You will most
likely want to use the script bp_bulk_load_gff.pl which should
have been installed when you installed BioPerl.
The full yeast genome is also available for download from Sourceforge.
features and yeast
DNA from the
gmod downloads page. You'll also find Worm, Fly and Human genome
annotations here, although not necessarily the most up to date ones.
Note that you will need to uncompress the data files prior to running
to load script. See the sample
configuration files directory for starter config files to get you
up and running.
Once you've loaded the yeast data (and adjusted the config file as
described in the INSTALL document), you can
browse the yeast genome by following the link http://localhost/cgi-bin/gbrowse/yeast.
To find out more about Gbrowse, try the:
Lincoln D. Stein, firstname.lastname@example.org
Cold Spring Harbor Laboratory
Last modified: Thu Jun 24 11:47:09 EDT 2004