[Bioperl-l] getting proteins matching GO

[Pedro Antonio Reche]

Dear Stefan, thanks a lot  for your e-mail. Actually, I am interested 
in getting all proteins from all organisms that are tagged with let say 
the go_process cell signaling. I will try the sites that you indicate 
to see if they can do the job. Do you know if Bioperl can also do this?
Regards,

pdro
On Nov 5, 2004, at 12:27 PM, Stefan Kirov wrote:

> What organism? You can use either EnsMart (for example for human there 
> is a table called hsapiens_gene_ensembl__xref_go__dm) or you can use 
> GeneKeyDB if you install it locally (genereg.ornl.gov/gkdb), there is 
> a table called ll_go, which you can search for the gene 
> identifier(locuslink), associated with a particular GO term and then 
> get the protein accession from another table  (something like : 
> "select r.np_accn from ll_go g, ll_refseq_nm r where r.ll_id=g.ll_id 
> and g.go_term=?") and fetch the seq from RefSeq, etc. Both Ensembl and 
> GeneKeyDB are restricted to certain eukaryotes. So it all depends on 
> what kind of organisms you are expected to work with.
> Stefan
>
> Pedro Antonio Reche wrote:
>
>> Hi,
>> I am interested in getting all the protein sequences  matching a 
>> specific GO term and I wonder if someone would know how to do this. 
>> Thanks in advance for any help.
>> Cheers
>>
>> pdro
>>
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>
>
> -- 
> Stefan Kirov, Ph.D.
> University of Tennessee/Oak Ridge National Laboratory
> 5700 bldg, PO BOX 2008 MS6164
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> fax +865-576-5332
> e-mail: skirov at utk.edu
> sao at ornl.gov
>
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>