[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.
> Pedro Antonio Reche wrote:
>> 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.
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
> 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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