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

James.Rose at UCHSC.edu James.Rose at UCHSC.edu
Thu Nov 9 17:56:00 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.



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