[Biopython-dev] Blastp for Proteins from Nematoda

[Peter Cock]

On Fri, Mar 21, 2014 at 4:30 PM, Brown, Tom <Tom.Brown at enmu.edu> wrote:
> How can I blastp a protein against only proteins from organisms in Nematoda (a phylum)?
>
> Thanks
>
> Tom

Hi Tom,

The two main options I can think of are:

1. Make a database of only nematode proteins - which is probably a good
idea anyway as many are not in NR, see also http://www.nematodes.org/

2. Search against the NCBI NR database doing a taxonomy filter, which
is possible if you use the -remote option and an Entrez filter (taxonomy
ID is 6231, so try txid6231[ORGN] as the Entrez filter).

Peter