[BioPython] BLAST SNP access?

[Michiel Jan Laurens de Hoon]

Zachary Zhipeng Sun wrote:
> 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.

It looks like that if you know the name of the database (here 
"snp/human_9606/human_9606"), then you can run for example

from Bio.Blast import NCBIWWW
result_handle = NCBIWWW.qblast("blastn", "snp/human_9606/human_9606", seq)

and then parse the results as usual (see section 3.4 in the Biopython 
tutorial).

Check on the page that Chris sent you:

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

to find the correct name for the database.

The result_handle should give you the same information as the web page, 
and Biopython's parser should parse all information from result_handle 
correctly. If you find that some information seems to be missing, please 
let us know.

Hope this helps,

--Michiel.

-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032