[Bioperl-l] organism restricted blast search

Aaron J. Mackey amackey at pcbi.upenn.edu
Thu Aug 5 12:20:31 EDT 2004

On Aug 5, 2004, at 12:03 PM, Jason Stajich wrote:

> I believe there are ways of building virtual subsets of the databases
> locally with some tricks with formatdb but I don't really know them.

You can make a file that has the GI numbers of the sequences you want 
to search against (say, a GI number dump from the Taxonomy DB), and 
then use "-l gilist" with NCBI blast tools

> You can also parse your reports and lookup the GI number using the 
> tools
> in Bio::Taxonomy and Bio::DB::Taxonomy to get the species name and or
> restrict hits to a particular subset of the taxonomy hierarchy.

This also works, but your expectation values will be artificially 
conservative (as you actually searched a potentially much larger 


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