Question
 
I'm looking for software you can use to download specific SNPs from
GENBANK together with specified flanking sequences and information about
other SNPs in that flanking sequence.  I know the software SNPhunter
(http://www.hsph.harvard.edu/ppg/software) does precisely this, but I am
looking for a program in which you can do batch queries for specific
SNPs using a file that lists SNPs according to their rs numbers.  The
batch queries of SNPhunter only involve genes, as far as I know, and my
SNPs are not associated with genes. 
 
 

Answer

 

I did not get any replies but found something that works for me on the
net @ http://snpper.chip.org/

You can specify the snps that you want in a batch list, and then get the
SNPs with specified lengths of flanking fragments and other snps in the
flanking parts in an output file.

You have to register to use the webpage.

 

Apparently SNPhunter can also handle SNP batch queries with rs numbers,
haven't tried it though

Hope this helps

Carina Schlebusch

Carina.Schlebusch@nhls.ac.za