Using Ubuntu 12.10 and the blastp command from the ncbi-blast+ package from the official repos, I want to query the remote ncbi database. So far, my command line looky like
$ blastp -db nr -query my-sequences.fa -remote -evalue 10e-3
and this gives me pretty much what i want. However on the BLAST Web interface i can specify a TaxID to narrow the search to an organism group (eg. taxid:2759 are eukaryota). I have found that blastn has a -windowmaskertaxid switch, but blastp does not seem to provide such a flag. How can i achieve this functionality in the command line tool?
Thanks in advance