[BioPython] PSI-BLAST using NCBIWWW

[Peter]

On Wed, May 7, 2008 at 10:02 PM, Katie Edmonds <betainverse at gmail.com> wrote:
> Hi,
>
>  I'm trying to use biopython to run psi-blast on the ncbi server.  It looks
>  like qblast cannot be used for psi-blast, and as far as I can tell blast()
>  doesn't work at all anymore, though it has a 'run_psiblast' parameter.  Has
>  anyone had success with running psi-blast with biopython who could offer
>  some advice?

I've done some investigation of using Bio.Blast.NCBIWWW.qblast() with
psi-blast, and it does seem to be missing the run_psiblast option.
However, I don't think that's the only issue here...

Have you been able to try running standalone psiblast, and parse its XML output?

Peter