[Bioperl-l] Fwd: Get variation included in genbank file

[Jessica Sun]

---------- Forwarded message ----------
From: Jessica Sun <jessica.sun at gmail.com>
Date: Wed, Jun 9, 2010 at 12:28 PM
Subject: Re: [Bioperl-l] Get variation included in genbank file
To: Dave Messina <David.Messina at sbc.su.se>
Cc: bioperl-l at lists.open-bio.org


I would need to automatically get a gbk file like this with
:Variation(dbSNP) included and correct mRNA/CDS regions, can it be done
automatically using
EUtilities<http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook>,
I am not sure about it.

thx



On Mon, Jun 7, 2010 at 5:18 PM, Dave Messina <David.Messina at sbc.su.se>wrote:

> Hi Jessica,
>
>
> > Does any know how to include variation(dbSNP) in the genbank file format
> > automatically using NM_ accession number using bioperl?
>
> I'm not sure I understand the question.
>
> As far as I know, Genbank records don't include SNP information. See for
> example the record for human p53 (which has SNPs):
>
>        http://www.ncbi.nlm.nih.gov/nuccore/NM_000546.4
>
>
> I think though you should be able to get to a dbSNP record if you have a
> NM_ accession number using the BioPerl interface to NCBI's EUtilities.
>
> More information here:
>
>        http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
>
>
> If that's not what you're after, could you clarify what you want to do?
>
>
> Dave
>
>


-- 
Jessica Jingping Sun



-- 
Jessica Jingping Sun
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