[Bioperl-l] getting proteins matching GO

Pedro Antonio Reche reche at research.dfci.harvard.edu
Fri Nov 5 17:25:30 EST 2004

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?

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
> Oak Ridge TN 37831-6164
> tel +865 576 5120
> fax +865-576-5332
> e-mail: skirov at utk.edu
> sao at ornl.gov
> "And the wars go on with brainwashed pride
> For the love of God and our human rights
> And all these things are swept aside"

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