Retrieving all genes of a species from DBBJ/GENBANK using Perl SOAP

[tomas_bar]

Hi,
I’m using Perl to query DBBJ using SOAP.
I want to find all genes of  a given species in the database.
However, the different SOAP services available like GetEntry only allow you to retrieve records by accession number.
Do you know how I could find all genes of a species?
Thank you very much.

[Fields, Christopher J]

Tomas,

Not sure if this is related to bioperl specifically.  Is there any  
particular you are using DDBJ over EMBL or GenBank?

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.

chris

On Nov 16, 2008, at 9:58 AM, tomas_bar wrote:

>
> Hi,
> I’m using Perl to query DBBJ using SOAP.
> I want to find all genes of  a given species in the database.
> However, the different SOAP services available like GetEntry only  
> allow you
> to retrieve records by accession number.
> Do you know how I could find all genes of a species?
> Thank you very much.
>
> --
> View this message in context: http://www.nabble.com/Retrieving-all-genes-of-a-species-from-DBBJ-GENBANK-using-Perl-SOAP-tp20520856p20520856.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[larymarquis]

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

[tomas_bar]

Hi

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.



tomas


On Mon, Nov 17, 2008 at 12:42 PM, larymarquis <rymarquis@...>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
>
> --
> View this message in context:
> http://www.nabble.com/Retrieving-all-genes-of-a-species-from-DBBJ-GENBANK-using-Perl-SOAP-tp20520856p20538720.html
>  Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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