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:

http://www.animalgenome.org/cgi-bin/gbrowse/

Directory Paths

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

GBrowse documentation, stylesheets and in-memory databases.

/doc/gbrowse

GBrowse configuration files

/conf/gbrowse.conf

GBrowse CGI (web) scripts

/cgi-bin/gbrowse
/cgi-bin/gbrowse_img
/cgi-bin/gbrowse_details
/cgi-bin/gbrowse_est
/cgi-bin/gbrowse_syn
/cgi-bin/gbrowse_moby

Online tutorial

http://www.animalgenome.org/gbrowse/tutorial/tutorial.html

Reference manuals

GBrowse Install HOWTO.

GBrowse Configuration HOWTO.

MAKE_IMAGES_HOWTO gives directions for creating stand-alone pictures with the gbrowse_img script

README-GFF-FILES describes methods for obtaining GBrowse compatible GFF files from WormBase, FlyBase, SGD and NCBI/human

PLUGINS_HOWTO gives directions for creating plugins

EADME-chado gives notes for using GBrowse with chado

DAS_HOWTO gives notes for using GBrowse as a Distributed Annotation System (DAS) server and client

ORACLE_AND_POSTGRESQL gives notes for running GBrowse on top of Oracle and PostgreSQL database servers

BIOSQL_ADAPTER_HOWTO has instructions for running GBrowse on top of a BioSQL database

GENBANK_HOWTO has notes for loading and browsing GenBank formated files

INSTALL.MacOSX has notes for installing GBrowse on MacOSX

Contributed modules and utilities

READMEs:

     README            README.berkeleydb
     README.fedora     README.gff3
     README.MacOSX     README.sessions
     README.Ubuntu

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 bp_load_seqfeature.pl 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 bp_bulk_load_gff.pl.

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

S. cerevisiae: SGD
D. melanogaster: FlyBase
C. elegans: WormBase
M. musculus (GFF2 only): MGD
R. rattus (GFF2 only): RGD
D. discoideum: Dictybase
H. sapiens (GFF2 only): HapMap
A. thaliana (GFF2 only): TAIR

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

Lincoln D. Stein, lstein@cshl.org
Cold Spring Harbor Laboratory

Last modified: Tue Mar 18 11:36:16 EDT 2008