[Bioperl-l] Get variation included in genbank file

Dave Messina David.Messina at sbc.su.se
Fri Jun 11 17:43:35 EDT 2010

On Jun 11, 2010, at 6:33 PM, Jessica Sun wrote:

> That was what I thought as well. It will be very nice that it can be done within bioperl as well.

Just to clarify, it can be done within BioPerl, but manually.

That is, you'll have to take the SNP information you have retrieved using the code Chris posted and then add it as features to the RichSeq object, which is BioPerl's internal representation of a Genbank record.

I don't think that this complicated set of procedures would fit very neatly into BioPerl as a more automatic thing, but of course if anyone is interested in coding it up we're more than happy to help find a place for it...


> On Fri, Jun 11, 2010 at 12:30 PM, Chris Fields <cjfields at illinois.edu> wrote:
> My guess is that NCBI has something that does this internally, and the result is either cached or run on-the-fly.  When I retrieved the full-length record from NCBI it lacked SNPs as well.
> chris
> On Jun 11, 2010, at 11:26 AM, Jessica Sun wrote:
> > Great ! Yet, how do you add this SNP as an Feature tag named as Variation
> > into the gbk file format automatically?
> >

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