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

larymarquis rymarquis at dbi.udel.edu
Mon Nov 17 07:42:28 EST 2008

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

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.  

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