[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
> 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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