[BioPython] Need help!!!

[Cymon J. Cox]

Hi Alper,

On Fri, 2006-04-21 at 00:07 -0700, alper soyler wrote:
> Hi Cymon,
>    
>   Thank you for your reply. However, to construct phylogenetýc profile I need to
>  download approx. 100 completed genomes. I am searching to make it easier (e.g.
>  without downloading genomes). Can I do it by running blast over the internet?

Well, I'm not sure; but here's my take on it and hopefully someone will
correct me if I'm wrong.

Assuming you are referring to complete genomes available through NCBI
(otherwise you'll almost certainly need to download them), I don't think
it's possible with the BioPython interface. Bio.Blast.NCBIWWW uses the
qblast interface at NCBI
(http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html) which I think only
makes the following db's available:
http://www.ncbi.nlm.nih.gov/blast/blast_databases.shtml . From looking
at the qblast docs it doesn't seem possible to restrict the search to a
particular organism while blast'ing against a particular NCBI db (e.g.
nr).

Depending on what you want to do, it maybe easier and quicker to use the
NCBI web Blast interface to the Genomes db's:
http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi

Else you'll have to bite the proverbial bullet and download and format
them individually.

Cheers, Cymon

>    
>   Regards,
>   Alper Soyler 
> 
> "Cymon J. Cox" <cy at cymon.org> wrote:
>   Hi Alper,
> 
> On Thu, 2006-04-20 at 05:59 -0700, alper soyler wrote:
> > Hi All,
> > 
> > I am new to Biopython and have a question. I want to construct a pyhlogenetic
> > profile for one organism's proteins. I want to give my protein to blast to
> > search one organism's genome (e.g. Homo sapiens) instead of whole genbank
> > database. How can I solve my problem? Thank you in advance.
> 
> Assuming you want to do this locally, you'll need to download you target
> genome, format it with the BLAST distribution programme 'formatdb', and
> then feed your query and newly formatted genome BLAST database to
> Bio.Blast.NCBIStandalone.
> 
> See http://biopython.org/docs/tutorial/Tutorial004.html#toc10
> 3.1.4 Running BLAST locally
> 
> for details,
> 
> Cheers, Cymon