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Running Blastp With Taxid

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

blast ncbi
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updated by lelle lelle • written by qselma • qselma

1 answer

You might want to have a look Vertebrate Subset Nr Database? Build My Own?

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written by lelle lelle

thanks, i didnt spot that. its a shame that you can't do this with the command line tool though. I think I will outsource the process into an Amazon EC2 instance eventually, so its not a big deal.

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written by qselma • qselma

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