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GO and PROSITE

Rolf Apweiler apweiler at ebi.ac.uk
Fri Apr 5 11:11:51 PST 2002


Hi Xinghua,
PROSITE is an InterPro member database. Nicola Mulder here at EBI has done a
mapping of InterPro entries to GO. See
ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro2go or
ftp://ftp.geneontology.org/pub/go/external2go/interpro2go. With a simple SRS
query you can do what you wanted: associate PROSITE patterns directly with GO
terms

I will send you the results file of the SRS query separately, since I do not
want to send it such a monster file to the whole mailing list.

Cheers

Rolf


=======================================================================
Rolf Apweiler                           | SWISS-PROT Coordinator
EMBL Outstation                         | Email:apweiler at ebi.ac.uk
European Bioinformatics Institute (EBI) | URL:  http://www.ebi.ac.uk
Wellcome Trust Genome Campus, Hinxton   | Tel:  +44 (1223) 494435
Cambridge CB10 1SD, UK                  | Fax:  +44 (1223) 494468
========================================================================



> Hi everyone,
>
> 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? Another question, is there such association that can be used
> as "golden standard" for me to evaluate my result?  Thanks a lot in advance.
>
> Cheers,
> Xinghua Lu
> M.D., Ph.D
> Center for Biomedical Informatics
>
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