Last Updated: February 5, 2002


We have developed a heuristic algorithm for associating 
molecular functions as defined by the Gene Ontology (GO) 
Consortium (See www.geneontology.org) to protein domains 
as listed in ProDom and CDD.  The algorithm generates 
'rules' for function-domain associations based on the 
intersection of functions assigned to gene products by 
the GO consortium that contain ProDom and/or CDD domains 
at varying levels of sequence similarity. 

Visit www.cbil.upenn.edu/GO to browse our rules and 
learn more about how we generated them.  

Each Release directory includes two subdirectories, 
"Rules" and "Predictions"  The contents of these
are described below.


Rules Directory		
================

From the Rules directory, you can download the 
learned domain-function associations.  These rules 
can be applied to predict GO molecular functions for 
novel protein/gene/transcript sequences based on 
similarity to one or more domains.  Note that we 
include a p-value threshold that can be used to help
avoid spurious function associations.  Accuracy of 
the Release 1 rules is estimated at 87% for ProDom 
and 84% for CDD rules (based on manual review of 
subset of rules).

For Release 1, we have generated four sets of rules:

     ProDom_NO_IEA
     ProDom_ALL

     CDD_No_IEA
     CDD_ALL

where NO_IEA indicates that we did not consider GO 
associations having only an IEA evidence codes. These
are associations that were generated with other 
computational methods and have not been manually 
reviewed yet.  A detailed description of the rule
files available for download is included in the Rules
directory.


Predictions Directory
=====================

From the Predictions directory, you can download GO 
associations we have generated based on the application 
of the above learned domain-function associations.  

For Release 1 of the rules, we have made GO function 
predictions for the following:

     musDoTS	(allgenes.org release 3.0)
     humDoTS  (allgenes.org release 3.0)

     SwissProt v39.22

     S.Cerevisiae
     A.Thaliana
     C.Elegans

Various combinations of rule applications were made.
See the ReadMe in the Predictions directory for a detailed
description.


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