[Biopython] Pulling Alignment From PSI-Blast Output

[Brett Bowman]

I thought about that, but there doesn't appear to be any multiple-alignment
data in the XML file - just pair-wise alignments of the query with each hit.
 In addition, when I parse the output file with NCBIXML I get a
Bio.Blast.Record.Blast object, instead of a Bio.Blast.Record.PSIBlast
object.  The Biopython cookbook describes how to work with a PSIBlast
object, but it doesn't really cover how to make one...

On Mon, Feb 7, 2011 at 5:20 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> One option you could try is to let PSI-Blast generate its output in XML and
> check if the information you need is present in the XML. If it is, you can
> parse the XML with the read() function in Bio.Entrez. You may find that
> Bio.Entrez needs an additional DTD file to be able to parse the PSI-Blast
> XML output (Bio.Entrez will tell you which one and where to store it). If
> so, please let us know, so we can include the required DTDs in the next
> release of Biopython.
>
> --Michiel.
>
> --- On Mon, 2/7/11, Brett Bowman <bnbowman at gmail.com> wrote:
>
> > From: Brett Bowman <bnbowman at gmail.com>
> > Subject: [Biopython] Pulling Alignment From PSI-Blast Output
> > To: biopython at biopython.org
> > Date: Monday, February 7, 2011, 5:30 PM
> > I'm trying to use the PSI-Blast
> > results from a series of proteins to detect
> > distant homologues, using HMMs of various sorts.
> > Currently I'm pulling down
> > the sequence IDs with PSI-Blast, downloading the full
> > sequences from NCBI,
> > then aligning everything with ClustalW or Muscle.
> > However this is eating up
> > way more processor time than I have to spare, so I want to
> > just pull the
> > full multi-sequence alignment from the PSI-blast results if
> > possible (OUTFMT
> > option #3 or 4), for use in building the HMMs.  But it
> > doesn't look like
> > AlignIO has a module for reading the peculiar format that
> > PSI-Blast
> > generates...
> >
> > Has this been done before, or will I need to write my own
> > parser?
> >
> > Brett Bowman
> > Woelk Lab
> > UCSD School of Medicine
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
>
>
>