[Biopython] PSI-BLAST help

[Steve Darnell]

Alaguraj,

I am assuming you have already downloaded the nr and env_nr databases.
You can create an alias database file that will tie individual databases
together to form a larger virtual database.

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html#4.1.
6

I have not personally used this approach, so I cannot offer more
guidance that this.  However, since biopython only provides a wrapper
for the NCBI command line tools, I would expect this approach would work
well with biopython scripting.

Regards,
Steve

--
Steve Darnell
DNASTAR, Inc.
Madison, WI USA


-----Original Message-----
From: biopython-bounces at lists.open-bio.org
[mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Matthew
Strand
Sent: Saturday, January 02, 2010 1:17 PM
To: Alaguraj Veluchamy
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] PSI-BLAST help

I'm no expert here but unfortunately you'll probably have to build your
own database to do that. It's not biopython's fault since it just wraps
PSI-BLAST and as far as I know PSI-BLAST is only made to search against
one database. Perhaps someone else will have a different solution.

On Fri, Jan 1, 2010 at 11:28 PM, Alaguraj Veluchamy
<alaguraj.v at gmail.com>wrote:

> Dear all,
> I have a problem in database search using PSI-BLAST.
> I have to do PSI-BLAST against combined "nr" and "environmental 
> sequences(env_nr)" databases.
> I need to iterate 10 rounds.
> Web services allow selecting one database at a time.
>
> Do Biopython offers search against multiple databases.
> I am unable to find any simple way to do this.
>
> Regards,
> Alaguraj.V