[BiO BB] SNP question

Annaiah, Kiran [BSD] - HGD kannaiah at bsd.uchicago.edu
Tue Nov 28 12:10:30 EST 2006


I have a bunch of SNPS (rs) and want to extract sequences 150bp upstream and downstream of it. I have used dbSNP database and have got the sequence info in FASTA format, although the length of the sequence(upstream and downstream) they return varies. Anywhere else i could go to get this info? I am looking at BIOMART and UCSC table browser right now. Havent figured it out yet.

Also when i get the 150bp sequence (up and downstream), i would like to know if any other SNP's exist in that region so i dont end up using that part of the sequence in my primer design process(end goal). Right now dbSNP does not tell me if there are any SNPs in the 150bp region around the SNP i submitted.

Any suggestions would be helpful.  

thank you

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