[BioPython] PSI-BLAST using NCBIWWW

[Peter]

On Thu, May 8, 2008 at 8:28 PM, Katie Edmonds wrote:
> From what I can get with the web interface, it seems like parsing the XML
> should be ok, though for however many iterations I try, it only seems to be
> giving me XML for iteration #1.

Could you try running standalone PSI-Blast and see how the XML output compares?

> I'm still trying to figure out how to run subsequent iterations of PSI-BLAST
> with your patch.

For anyone else interested, see
http://bugzilla.open-bio.org/show_bug.cgi?id=2496

> In the web form it seems to keep track of all past iterations with NEXT_I:
>
> <input name="NEXT_I" type="hidden" value="Run PSI-Blast iteration 2">
>
> <input name="NEXT_I" type="hidden" value="Run PSI-Blast iteration 3">
>
> <input name="NEXT_I" type="hidden" value="Run PSI-Blast iteration 4">
>
> I don't have any idea how similar the qblast interface is to the web
> interface, though.
>
> Thanks,
>
> Katie

You are talking about multiple iterations of results from a single
query?  Looking at the example output I got yesterday, there is indeed
only one iteration present.  I know that multiple queries in classic
blast or RPS-Blast get returned in the XML file as different
iterations, which may be complicating things.

Would you like to email the NCBI directly and ask if PSI-Blast is
intended to be used by a program via the QBLAST API CGI page?  They
may have some tips.

Peter