[Bioperl-l] eutils help

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Dec 6 14:48:28 EST 2010


I do this quite frequently and it's usually easiest to download the flanking fasta for the SNPs with their batch query tool http://www.ncbi.nlm.nih.gov/SNP/batchquery.html then trim the sequences as required with BioPerl.
I think you'll run into problems downloading that many SNPs reliably with eUtils and it's best to break it up into smaller chunks.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of kris richardson
> Sent: Tuesday, 7 December 2010 6:17 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] eutils help
> 
> Dear Bioperl Users,
> 
> I am interested in generating the flanking sequences (20 nt from each
> side) from a list of ~500,000 SNPs, from the dbSNP build 132.
> 
> I tried using the perl API variation toolset to extract this
> information, however the script throws an error when it encounters many
> of the recently discovered SNPs (from the 1000genomes data), as this
> tool is still using the dbSNP 131 data.
> 
> I read the bipoerl eUtils tool  might be used to obtain this info, but
> I can not find any example code in which the dbSNP data is queried...
> Does any one have any pointers or examples on how one might use efetch
> and eUtils  to obtain the flanking sequence for a list of SNP rs #s?
> 
> 
> Thanks!
> 
> Kris
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