[Biopython] Pulling Alignment From PSI-Blast Output

[Brett Bowman]

I had never heard of jackHMMER until now, so I'll look into it.  However the
outline of my current project is essential "This paper used X to find Y, so
I want you to use X to find a homologue of Y in this other background", so
I'm not sure how much wiggle room I have to change the methodologies used.
 The source paper used HHmake to create HMMs from the output of PSI-Blast,
so I am trying to do the same if possible.

-Brett

On Mon, Feb 7, 2011 at 9:41 PM, Ruchira Datta <ruchira.datta at gmail.com>wrote:

> If you're using HMMs anyway, why not use jackhmmer?  It's been shown to be
> more sensitive than PSI-BLAST at the same number of iterations, and with an
> option it will output the alignment.
>
> Note that its alignment is in Stockholm format though, and if you want
> something else, BioPython's Stockholm parsing is very slow.
>
> --Ruchira
> On Feb 7, 2011 2:31 PM, "Brett Bowman" <bnbowman at gmail.com> wrote:
> > 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
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>