[Biopython] PSI-BLAST

[Senthil Kumar M]

On Sun, Jul 17, 2011 at 2:53 PM, malvika sharan <malvikasharan at gmail.com> wrote:
> Hi All,
>
> I am trying to code WWW version of PSI-BLAST. My intention is to integrate
> PSI-Blast in my tool in order to find distant homologs.
>
> i some how can not run the commandline version of psi blast (from
> Bio.Blast.Applications import *NcbipsiblastCommandline*) as it states the
> error
> *" **Python* error: ImportError: *cannot* import *name
> **NcbipsiblastCommandline
> "*
> *
> *
> *There are not much information available about it. Can somebody figure out
> why?*
> *
> *
> *Malvika*
> *
> *

Hi,

According to the Biopython tutorial
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc93 (2 April
2011 version):

"You can run the standalone verion of PSI-BLAST (the legacy NCBI
command line tool blastpgp, or its replacement psiblast) using the
wrappers in Bio.Blast.Applications module.
At the time of writing, the NCBI do not appear to support tools
running a PSI-BLAST search via the internet."

HTH,

Senthil

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