[Bioperl-l] GenBank Feature: variation

Brian Osborne osborne1 at optonline.net
Wed Jun 7 11:42:32 EDT 2006


Nicolaus,

The short answer is no, there's no option that will omit or add a particular
feature or annotation to the Sequence object returned by Bio::DB::GenBank.
Can you give some example accessions?

Brian O.


On 6/7/06 9:46 AM, "Nicolaus Hepler" <nlhepler at umd.edu> wrote:

> Hello,
> 
> I am having some difficulty here.  I have a list of accessions, which
> are the parameters for a get_Stream_by_acc() function on a
> Bio::DB::GenBank object.  None of the returned GenBank information
> for any of my accessions seems to contain variation data, no matter
> how I try to coax it out with unflattener and typemapper.  This data
> is, however, available via the web interface of NCBI Nucleotide, as
> an optional feature (SNP).  I was wondering if there was some option
> I'm missing in the initialization of the Bio::DB::GenBank object (no
> options currently) that will coax the database into giving me this
> data?  Or something else that I'm missing altogether.  The organism
> of interest is human, taxon:9606.
> 
> Nicolaus Lance Hepler
> nlhepler at mail dot umd dot edu
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