[Bioperl-l] Remote tblastn against a sequenced genome at NCBI

[Chris Fields]

> Hi- apologies if this subject has been addressed before, but I  
> can't seem to find a way to search prior threads short of  
> downloading the entire archives. I'm trying to use Bioperl to do  
> something I thought would be fairly simple:
>
> Ingredients: one file containing a list of GI numbers for various  
> proteins
>
> 1) Read GI number from file.
> 2) run a remote tblastn search against the sequenced Spermophilus  
> tridecemlineatus genome with the GI number as query.
> 3) save resultant BLAST file to disk for later parsing.
>
> As it stands, several hours of browsing and scripting has failed to  
> turn up anything that might be useful in this regard.
>
> Any advice is very much appreciated.
>
> Thanks,
>
> James

NCBI has a little-known (but very useful) list of databases available  
for remote BLAST searches:

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

If you replace the database parameter with the exact string listed  
under the table, then it should work.  'Trace/ 
Spermophilus_tridecemlineatus_WGS' for the WGS sequences is probably  
what you want.

Chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign