[Bioperl-l] GenBank Feature: variation

Nicolaus Hepler nlhepler at umd.edu
Wed Jun 7 09:46:32 EDT 2006


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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