Generic Genome Browser

Welcome to the Generic Genome Browser!

Example Database

An example in-memory database for S. cerevisiae chromosomes 1 and 2 has been installed for you. Try it at this URL:


Directory Paths

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

GBrowse documentation, stylesheets and in-memory databases.
/var/www/html/gbrowse (also available for browsing at http://localhost/gbrowse)

GBrowse configuration files

GBrowse CGI (web) scripts

Online tutorial
/var/www/html/gbrowse/tutorial (available for browsing at http://localhost/gbrowse/tutorial/tutorial.html).

Reference manuals
GBrowse Install HOWTO.

GBrowse Configuration HOWTO.

/var/www/html/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).

/var/www/html/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).

/var/www/html/gbrowse/docs/pod/PLUGINS_HOWTO.html gives directions for creating plugins (at http://localhost/gbrowse/docs/pod/PLUGINS_HOWTO.html).

/var/www/html/gbrowse/docs/pod/README-chado.html gives notes for using GBrowse with chado (at http://localhost/gbrowse/docs/pod/README-chado.html).

/var/www/html/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).

/var/www/html/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).

/var/www/html/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).

/var/www/html/gbrowse/docs/pod/GENBANK_HOWTO.html has notes for loading and browsing GenBank formated files (at http://localhost/gbrowse/docs/pod/GENBANK_HOWTO.html).

/var/www/html/gbrowse/docs/pod/INSTALL.MacOSX.html has notes for installing GBrowse on MacOSX (at http://localhost/gbrowse/docs/pod/INSTALL.MacOSX.html).

Contributed modules and utilities


More Data Sets

Chromosomal annotations are described using GFF3 files, which usually have the suffix .gff or .gff3. To load larger data sets it is suggested that you create a MySQL database and use the script which should have been installed when you installed BioPerl. Some databases may use the older GFF2 format, in which case you should load using

You will find suitable data files at the following model organism databases:

S. cerevisiae
D. melanogaster
C. elegans
M. musculus (GFF2 only)
R. rattus (GFF2 only)
D. discoideum
H. sapiens (GFF2 only)
A. thaliana (GFF2 only)

Check the contrib directory for contributed configuration files for some of the common model organisms.

Lincoln D. Stein,
Cold Spring Harbor Laboratory
Last modified: Tue Mar 18 11:36:16 EDT 2008