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

[Chris Fields]

On Nov 9, 2006, at 4:56 PM, <James.Rose at UCHSC.edu> wrote:

>
>
> 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

Oops, sent you an old page.  Here's the more up-to-date one:

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

Chris

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