[Bioperl-l] Re trieving all genes of a species from DBBJ/GENBANK using Perl SOAP

bar tomas bartomas at gmail.com
Tue Nov 18 05:45:46 EST 2008


Thank you very much for your replies, and sorry that my post was misplaced
in this forum.

I'm pretty clueless on this subject. My difficulty is that my aim is to
retrieve all gene names of a given species and that the when performing a
query on a species name, I get a list of accession numbers. Can a record
identified by an accession number span several genes? Can a record
identified by an accession number refer to a sequence that is not a gene?

My choice of using DDBJ is pretty uninformed too. I had understood that the
information contained in DDBJ includes Genbank and I was interested in the
DDBJ facility of performing XPath queries on GenBank entries. But do you
recommend using NCBI Entrez instead?

Thank you very much and sorry about my clueless questions.


On Mon, Nov 17, 2008 at 12:42 PM, larymarquis <rymarquis at dbi.udel.edu>wrote:

> Chris Fields-5 wrote:
> >
> >
> > I would probably go about this using Bio::DB::GenBank,
> > Bio::DB::EntrezGene, or similar in combination with a GenBank query
> > (Bio::DB::Query::GenBank); see the relevant module POD for details.
> >
> >
> If you are using NCBI, the Taxonomy browser in NCBI is a good way to
> identify the appropriate query term to obtain all the sequences for a given
> species.
> You can navigate to your species in the Taxonomy tree and select what
> databases you want to query from the check boxes at the top.  After hitting
> the go button, it will display the number of sequences meeting the
> criteria.
> Clicking on the number will send you to the normal results page except a
> keyword has been filled in for you (something like txid3052[Organism:exp]
> ).
> You can then use this keyword to access the entire set of sequences using
> EFETCH from NCBI and maybe the bioperl modules as well.
> Linda
> --
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