[Bioperl-l] getting proteins matching GO
skirov at utk.edu
Fri Nov 5 12:27:35 EST 2004
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
e-mail: skirov at utk.edu
sao at ornl.gov
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