[Bioperl-l] Get variation included in genbank file

[Jessica Sun]

Thanks Dave.
the variation information is not present in the version of NG_011506 I found
at Genbank.) -- Yes, then if you click on the right side customer view there
is a check box Features added by NCBI :209 snps, if you check that it will
add all the variations in the gbk fomat. I found this would be a neat
feature if it can automatically load by bioperl with an option turn on.



On Wed, Jun 9, 2010 at 1:51 PM, Dave Messina <David.Messina at sbc.su.se>wrote:

> Hi Jessica,
>
> Please keep the BioPerl list on the Cc line so everyone can follow along.
>
>
> > Follow your approach it did not seem to me you can have Variation tag
> included which
> > list the know dbSNP location, id and allele changes?
>
> Ah okay, I assumed the file you attached was obtained directly from Genbank
> and that the variation info therein was already included. (It appears that's
> not the case — the variation information is not present in the version of
> NG_011506 I found at Genbank.)
>
> If you want to include your own custom information in a genbank file,
> you'll have to pull it out of dbSNP (or wherever the variation info is).
> There are a couple of scripts that might be able to help with that (search
> for snp):
>
>        http://www.bioperl.org/wiki/Bioperl_scripts
>
>
> You can then insert them into a RichSeq object as features and output in
> genbank format. For that part, see the HOWTO:
>
>        http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
>
> Dave
>
>


-- 
Jessica Jingping Sun