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GO and PROSITE

Wolfgang Fleischmann iwfl at mac.com
Fri Apr 5 10:44:34 PST 2002


Hi Xinghua,


On Friday, April 5, 2002, at 07:24 , Xinghua Lu wrote:
> The current GO sequnce files have PROSITE and other sequence patterns
> associated with them.  I am try to develop a method to associate the GO 
> term
> with PROSITE patterns directly.  In another word, assign a GO term to 
> the
> patterns, so that people can search the GO for patterns too.  Has this 
> been
> done by anyone?

PROSITE is part of InterPro, see www.ebi.ac.uk/interpro for details.
Nicky Mulder started to map InterPro entries to GO terms. As all PROSITE
patterns have exactly one InterPro accession, her mapping can be 
translated
easily from InterPro -> GO to PROSITE -> GO. If you have difficulties 
doing
that, mail again, we surely can help with that.

Similarily, searching for PROSITE patterns is part of searching for 
InterPro
entries. You can use this online or download and install at your site. 
"InterProScan"
has an option to do the mapping to GO terms. Input is a aminoacid 
sequence,
output are GO terms.

>  Another question, is there such association that can be used
> as "golden standard" for me to evaluate my result?  Thanks a lot in 
> advance.

Well, I don't know if we claim to be the standard, but Nicky's 
interpro2go mapping
is done manually and carefully inspected.

To retrieve the InterPro to GO mappings, go either to 
www.ebi.ac.uk/interpro and
follow the link to 'List of InterPro to GO mappings", or go to 
www.geneontology.org
and scroll down to 'Indices of other Classification systems to GO'.

Cheers,
Wolfgang


Wolfgang Fleischmann
EMBL Outstation - The EBI       e-mail: fleischmann at ebi.ac.uk
Wellcome Trust Genome Campus     phone:    +44 (0)1223 494406
Hinxton, Cambridge CB10 1SD, UK    fax:    +44 (0)1223 494468


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