[BioPython] BLAST SNP access?

[Chris Fields]

If you are using the NCBI URLAPI interface you can set the databases  
to anything on the following page, just follow the instructions:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/ 
remote_accessible_blastdblist.html

This includes SNP data.  I find this works for BioPerl's RemoteBlast  
(URLAPI-based).

chris

On Mar 21, 2007, at 11:21 PM, Michiel de Hoon wrote:

> Hi Zach,
>
> Can you give us an example of how you currently query the BLAST SNP
> database (without using Biopython)? Just to get an idea of how  
> different
> it is from current BLAST searches with Biopython.
>
> --Michiel.
>
> Zachary Zhipeng Sun wrote:
>> Hello,
>>
>>
>>
>> Thank you for the Bioython tools! They are proving increasingly  
>> useful in my
>> research. I had a question regarding a tool extension, however -  
>> is there
>> any link in biopython to query the BLAST SNP database, or does  
>> anyone know
>> of this being under development? If not, I am not too familiar  
>> with the
>> backend of biopython but I was looking to be able to automate  
>> BLAST SNP
>> searches; does anyone have advice on how to start coding this into  
>> the
>> biopython environment, or to a version of NCBIWWW.py ? Thanks for  
>> your help!
>>
>>
>>
>> Best,
>>
>> Zachary Sun
>>
>>
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign