[BiO BB] may I use GO to identify functional similar proteins
cjm at fruitfly.org
Wed May 28 17:21:42 EDT 2008
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.
> 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.
> On 28-May-08, at 2:37 PM, Xue Li wrote:
>> Hello all,
>> Does anyone know whether I could use GO to identify functional
>> 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
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>> BBB at bioinformatics.org
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