FUNC README


1. INTRODUCTION

This README file comes along with the source of FUNC. It contains
general information about this package. If you are looking for
installation instructions see the INSTALL file. You can find further 
information regarding the implementation in the file src/doc/HACKING.

FUNC is a set of 4 tools to analyse gene data using the Gene Ontology
database. To keep the programs as compatible as possible, it needs the
Gene Ontology structure as well as the mapping of the genes to the
Gene Ontology.

These package contains Free Software. Please see the COPYING file
placed in the same directory as this file for copying information.



2. MAPPING GENES TO GENE ONTOLOGY

The Gene Ontology website (http://geneontology.org/) has a listing of
all annotations to the gene ontology. Tools like Ensembl BioMart
(http://www.ensembl.org/Multi/martview) can help a great deal, too.
You can look at the following websites to find mappings:

Affymetrix          - www.affymetrix.com
LocusLink           - ftp.ncbi.nih.gov/refseq/LocusLink
Unigene             - www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene



3. DOWNLOADING THE GO TERMDB TABLES

You can download different releases of the Gene Ontology database from
http://www.godatabase.org. The archives are located at:

http://archive.geneontology.org/full/

Choose the appropriate release (fitting the mapping of your data) and
download the file 

        go_[date]-termdb-tables.tar.gz

Extract it using the command

        tar -vxzf go_[date]-termdb-tables.tar.gz

The directory go_[date]-termdb-tables must be passed as an argument to 
the func programs.



4. WHAT ELSE

Please have a look at the manpages with

	man func

to learn more about the invocation of the tools, the input format and
the output. Probably you will also find more information in the 
documentation directory for this program (i.e. /usr/local/doc/func-VERSION)