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Generic Genome Browser

Welcome to the Generic Genome Browser!

Example Database

An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:

http://localhost/cgi-bin/gbrowse/yeast_chr1

Directory Paths

For future reference, here is where you've installed GBrowse's various components:

GBrowse documentation, stylesheets and in-memory databases.
/bio/argos/common/perl/gbrowselive/htdocs/gbrowse (also available for browsing at http://localhost/gbrowse)

GBrowse configuration files
/bio/argos/common/perl/gbrowselive/conf/gbrowse.conf

GBrowse CGI (web) scripts
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse_img
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse_details
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse_est
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse_syn
  • /bio/argos/common/perl/gbrowselive/cgi-bin/gbrowse_moby

Online tutorial
/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/tutorial (available for browsing at http://localhost/gbrowse/tutorial/tutorial.html).

Reference manual
/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/INSTALL.html (available for browsing at http://localhost/gbrowse/docs/pod/INSTALL.html).

/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/CONFIGURE_HOWTO.html (available for browsing at http://localhost/gbrowse/docs/pod/CONFIGURE_HOWTO.html).

/bio/argos/common/perl/gbrowselive/htdocs/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).

/bio/argos/common/perl/gbrowselive/htdocs/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).

/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/PLUGINS_HOWTO.html gives directions for creating plugins (at http://localhost/gbrowse/docs/pod/PLUGINS_HOWTO.html).

/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/README-chado.html gives notes for using GBrowse with chado (at http://localhost/gbrowse/docs/pod/README-chado.html).

/bio/argos/common/perl/gbrowselive/htdocs/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).

/bio/argos/common/perl/gbrowselive/htdocs/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).

/bio/argos/common/perl/gbrowselive/htdocs/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).

/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/GENBANK_HOWTO.html has notes for loading and browsing GenBank formated files (at http://localhost/gbrowse/docs/pod/GENBANK_HOWTO.html).

/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/docs/pod/INSTALL.MacOSX.html has notes for installing GBrowse on MacOSX (at http://localhost/gbrowse/docs/pod/INSTALL.MacOSX.html).

Sample data
/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/sample_data.txt

Contributed modules and utilities
/bio/argos/common/perl/gbrowselive/htdocs/gbrowse/contrib

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. Get yeast 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.

Learning More

To find out more about Gbrowse, try the:


Lincoln D. Stein, lstein@cshl.org
Cold Spring Harbor Laboratory
Last modified: Thu Jun 24 11:47:09 EDT 2004

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