[Bioperl-l] Need help for a GO request

Brian Osborne brian_osborne at cognia.com
Thu Oct 6 21:19:44 EDT 2005


There are different approaches, depending on what your accessions are. If
your accessions are Locus/Gene ids from LocusLink/Entrez Gene then simply
use the "entrezgene" format of SeqIO. If your accessions are Genbank
nucleotide then you may be able to find the corresponding Entrez Gene ids by
parsing the gene2accession file of Entrez Gene yourself, there is no module
to do this in Bioperl but it will be easy. With these in hand you'll, again,
use SeqIO and entrezgene to find the corresponding GO terms.

You'll notice that my suggestions center around Genbank and Entrez Gene, but
there are other databases that assign GO terms besides these.

If you're new to Bioperl then taking a look at various HOWTOs could be
useful (bioperl.org/HOWTOs).

Brian O.

On 10/6/05 11:11 AM, "ctemp2 at free.fr" <ctemp2 at free.fr> wrote:

> Hello,
> I have a list of genes (accession numbers) and I would like to find the
> associated informations in Gene Ontology (I work with those datas, find
> biological process, common node between 2 genes...).
> I am a newbie with Bioperl and I would like to know :
> - if there would be a module to send a request to the NCBI to obtain the GO
> informations for those genes
> - or if there would be a module to send the GO id to the GO site (I tried to
> use
> Bio::Ontology::SimpleGOEngine but the example doesn't work, I get an error
> with
> the 'parse' method which is not found by Perl in the module).
> Thanks if you can help me.
> Regards.
> C. Tobini
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