[pombelist] Functioanl Classification

Valerie Wood val at sanger.ac.uk
Wed Oct 13 09:43:07 EST 1999


S. pombe Functional Classification
----------------------------------

The preliminary Functional catalogue is now accessible
from the S. pombe homepage:

http://www.sanger.ac.uk/Projects/S_pombe/fun_class.shtml

http://www.sanger.ac.uk/Projects/S_pombe/
        
This will (when complete) enable comparisons with S. cerevisiae to 
be made by functional category.
You can cross reference against the yeast functional classification at:

http://www.mips.biochem.mpg.de/proj/yeast/catalogues/funcat/index.html

The initial classification process is automated, classifying proteins
by gene name, EC number and product description, by comparing to 
curated sets of names and keywords. However, further curation is manual
to provide more accurate assignments.

If you notice any errors in specific assignments (or ommissions) please 
mail the curator listed at the bottom of the page. We would also welcome 
offers for curation of the unassigned classes.

The transporter class has been fully curated based on a complete
analysis of the partial protein set by Ian Paulson. We can already see
by extrapolation that pombe will probably have fewer transporters than
S. cerevisiae (~200 vs 303)

Other classes also show large differences in numbers when compared to 
yeast, but at present this is mainly due to the lesser degree of 
characterisation in pombe.

There is also an alternative pombe classification at Pedant, 
(recently updated to 3816 proteins). 
This is based on homology to the proteins in the yeast catalogue, and
may therefore be useful for the identification of candidate genes in
your area of interest.
You can access this at:
  
http://pedant.mips.biochem.mpg.de/
follow the links....
         Schizosaccharomyces pombe
                Yeast FUNCAT


We consider these two data-sets to be complementary. Our version will
develop into a fully curated classification, while Pedant will provide
additional putative assignments based on homology rather than critical
assessment of the annotated function.

Pombe Team Curators
Mike Lyne -Mitosis
Rachel McDougall- RNA processing
Valerie Wood - Transporters

We would also like to acknowledge the contributions of the following
people:

Ian Paulson - Transporters
George Shpakovski -Ribosomal Protein Inventory
Norbert F. Kaeufer -Ribosomal Protein Inventory


-- 
----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. Pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Centre              email: val at sanger.ac.uk
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe 
Cambridge                      S. pombe Functional Classificatiom
CB10 1SA                       http://www.sanger.ac.uk/Users/val/





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