[BioPython] BLAST SNP access?

[Zachary Zhipeng Sun]

Thanks for the replies! Regarding a BLAST SNP search, it uses the blastn or
tblastn interface; put in query at
http://www.ncbi.nlm.nih.gov/SNP/snp_blastByOrg.cgi, choose db, and result
interface is similar to other BLAST components. (sample RID
1174538798-721-146214187572.BLASTQ2 for sample output), except that in the
title of hits it shows an rs# which links to dbSNP. I'd imagine the search
options would be different, as well as a little bit of parsing the output,
but it uses the same engine as blastn.

Regarding the URLAPI then: sorry, I'm pretty new to biopython, but is the
qblast search feature in the current biopython 1.43 build based on commands
to the NCBI URLAPI? If so, then (from someone with moderate experience in
coding but little in python or perl) would I be able to painlessly modify
the biopython NCBIWWW.py code for my own use?

-Zach

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Thursday, March 22, 2007 12:38 AM
To: Michiel de Hoon
Cc: Zachary Zhipeng Sun; biopython at lists.open-bio.org
Subject: Re: [BioPython] BLAST SNP access?

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