[Bioperl-l] Downloading from dbEST by taxon range

Albert Vilella avilella at gmail.com
Sat Jan 2 03:57:28 EST 2010


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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