[Bioperl-l] eutils help

kris richardson kris.richardson at tufts.edu
Mon Dec 6 12:16:58 EST 2010


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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