[BioPython] PSI-BLAST using NCBIWWW
Peter
biopython at maubp.freeserve.co.uk
Thu May 8 11:37:34 UTC 2008
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
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