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

Chris Fields cjfields at uiuc.edu
Thu Nov 9 19:46:35 EST 2006

> 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:


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.


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

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