[Bioperl-l] Limiting organism scope on bioperl BLAST searches

Dave Messina David.Messina at sbc.su.se
Mon Jun 16 13:35:53 EDT 2008

Hi Nathan,

It's not clear from your script whether you are doing your BLAST search
locally with the database on your own computer or whether you're doing a
netblast (blastcl3) where the database is on the NCBI server.

If the latter, you can use the -u option to limit your search to the results
of an Entrez query. See the blastcl3 manual on NCBI's website for details; I
think there's even an example for this very purpose.

If the former, you could create a database with sequences from the 5
mammalian species. There are lots of ways to do that, but I usually do an
Entrez search crafted to my purpose and download the FASTA sequences. Or you
could do the same thing at Ensembl, either via the website or via the Perl


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