[Biopython] PSI-BLAST

[Peter Cock]

Hi Lluís,

Something was added to the NCBIWWW docstrings as a result of
a user contribution, but I'm as much in the dark as you are about
what options if any the NCBI support for doing PSI-BLAST online:

https://github.com/biopython/biopython/pull/12

I would personally download the NCBI BLAST+ binaries and
run the command line psiblast tool (perhaps via the Biopython
command line wrapper).

The PSIBlast record you are talking about is from the plain text
parser Bio.Blast.NCBIStandalone.PSIBlastParser, right now our
BLAST XML parser and the SearchIO equivalent does not really
handle PSI BLAST.

I thought there was a recent GitHub issue about parsing the psiblast
output, but I can't seem to find it...

Peter

On Tue, Mar 15, 2016 at 1:45 PM, Lluís Revilla <lluis.revilla at gmail.com> wrote:
> Hello!
>
> I am trying to perform online a PSI-BLAST. In the tutorial there isn't any
> example so looking on the help I found what I thought it was the way:
>
> record = SeqIO.read("protein.fasta", format="fasta")
> result_handle = NCBIWWW.qblast('blastp', 'nr', record.format("fasta"),
>                                     service='psi')
> blast_record = NCBIXML.read(result_handle)
>
> However it returns a normal Blast record. But the object I get is not the
> "PSIBlast record " described on the tutorial with information about. I
> haven't found the way to set the number of round of the PSI-BLAST (neither
> in the NCBI help at http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html ).
>
>
> How can I do a PSI-BLAST?
>
> Many thanks,
>
> Lluís
>
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