[Bioperl-l] GenBank Feature: variation

Nicolaus Hepler nlhepler at umd.edu
Wed Jun 7 12:26:06 EDT 2006


A sample accession is BC000007.  I figured a way around it though.   
Rather than automate the whole process, I just downloaded from Batch  
Entrez a flat .gb file of all my accessions.  It's not flexible, and  
will be inconvenient when we expand the dataset, but it will provide  
me with data to work with for now.


> 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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>> Bioperl-l at lists.open-bio.org
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