[Biopython] local taxonomy search

[Xie, Boya]

Hi Peter,

Thank you for your reply!

What I want is giving an species name or gi number, find which kingdom, class, phylum, order, family it belongs to. And I want to do this locally.

Thanks,

Tina
________________________________________
From: p.j.a.cock at googlemail.com [p.j.a.cock at googlemail.com] On Behalf Of Peter [biopython at maubp.freeserve.co.uk]
Sent: Saturday, June 20, 2009 2:53 PM
To: Xie, Boya
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] local taxonomy search

On Sat, Jun 20, 2009 at 7:27 PM, Xie, Boya<BX1030 at ecu.edu> wrote:
> Hi
>
> Does anyone know a way to perform taxonomy search
> against either ncbi taxonomy database or your own
> database LOCALLY? like the blast, Biopython provides
> both over internet and local option: Bio.Blast.NCBIWWW
> and Bio.Blast.NCBIStandalone.
>
> Thank you!

Hi Tina,

I don't understand exactly what you are asking for.

Do you want to be able to search for a species name
and find out the NCBI taxonomy ID for it? Or the other
way round, given an NCBI taxonomy ID get the species
name?

Are you asking how to do a BLAST search locally using
a taxonomy filter?

Or something else? Perhaps you could give an example
search term and what result you want back.

Peter