[Bioperl-l] Downloading from dbEST by taxon range

Jason Stajich jason at bioperl.org
Sat Jan 2 11:35:22 EST 2010


DId you try Bio::DB::Query::GenBank ?
You'd want to use -db => 'nucest' and then you just put in an Entrez  
query as per the example.  you can include dates in the query so you  
can do updates to your locally retrieved data in a script that runs  
periodically.

-jason
On Jan 2, 2010, at 12:57 AM, Albert Vilella wrote:

> Hi all and happy 2010 for those that follow the Gregorian calendar,
>
> A question that is a bit in between bioperl and NCBI. I would like  
> to use
> bioperl to download sequences fom dbEST. For that, my idea is to use
> Bio::DB::Genbank and get the sequences by gi id.
>
> Now, I want my script to download sequences for a given NCBI  
> taxonomy clade.
>
> For example, if I want to download all fish (clupeocephala)  
> sequences in dbEST,
> I can browse it around with the dbEST webpage using  
> "clupeocephala[taxonomy]",
> so I am thinking there should be a way to do it programmatically.
>
> How can I query NCBI dbEST through bioperl to give me the list of GI  
> ids I am
> looking for given a taxon id?
>
> Thanks in advance,
>
> Albert.
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/



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