[Biopython-dev] Blastp for Proteins from Nematoda

[Brown, Tom]

Peter,

Thanks. It is working.

Tom

-----Original Message-----
From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
Sent: Friday, March 21, 2014 10:35 AM
To: Brown, Tom
Cc: Biopython-dev at lists.open-bio.org
Subject: Re: [Biopython-dev] Blastp for Proteins from Nematoda

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

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