[BioPython] blast against genomes, was: Need help!!!

[Peter (BioPython)]

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?

So you want to search 100 completed genomes using your protein as the 
input query?

As Cymon suggested, downloading the genomes and building your own 
database is one method.  As this is a "big task" you have in mind, the 
network speed limitations of doing many blast queries may make this a 
better idea than trying to do it online.

However, the NCBI offer online blast against some (all?) of their 
completed genomes so it may be possible to do it this way via BioPython.

http://www.ncbi.nlm.nih.gov/BLAST/

The webpage has a nice interface for blast against specific genomes 
(right hand side, second box down).

You can also use the normal blast pages and the "Limit by entrez query" 
field, e.g. mouse[ORGN] OR rat[ORGN]

It should be possible to do this automatically in code but you will need 
to compile a list of the species names the NCBI will understand...

Peter