[BiO BB] may I use GO to identify functional similar proteins

[Chris Mungall]

See also:

http://www.geneontology.org/GO.tools.shtml

The developers of many of these tools hang out on the gofriends list,  
you may want to ask there too:
gofriends at genome.stanford.edu

On May 28, 2008, at 12:32 PM, Boris Steipe wrote:

> A number of similarity measures on GO have been defined in the
> literature. Once you have a PDB ID, get the corresponding UniProt ID,
> then use FunSimMat to find other proteins of similar function. The
> authors discuss the concepts and pitfalls of such an approach in
> their 2007 NAR paper.
>
>     http://funsimmat.bioinf.mpi-inf.mpg.de/
>
> However this approach does not really operate on independent data: a
> very large number of GO annotations is "inferred from electronic
> annotation" - i.e. more or less from a BLAST search. You are likely
> to get very similar information by simply doing a BLAST (or VAST)
> search in the first place: homologous proteins have similar function.
> But try it, it's quite informative.
>
> HTH,
> Boris
>
>
> On 28-May-08, at 2:37 PM, Xue Li wrote:
>
>> Hello all,
>>
>> Does anyone know whether I could use GO to identify functional  
>> similar
>> proteins? Given a protein pdbID, can I search GO for functional
>> similar proteins? Thanks.
>>
>> -- 
>> Xue, Li
>> Bioinformatics and Computational Biology program @ ISU
>> Ames, IA 50010
>> 515-450-7183
>>
>> _______________________________________________
>> BBB mailing list
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>