[Biopython] Pulling Alignment From PSI-Blast Output

[Ruchira Datta]

Oh, I see what you mean.  Yes, I've had issues with HHmake on HMMER HMMs, so
I'd stick with your current protocol and let it make HMMs the way it wants
to.

--Ruchira

On Mon, Feb 7, 2011 at 11:44 PM, Brett Bowman <bnbowman at gmail.com> wrote:

> 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
>> > _______________________________________________
>> > Biopython mailing list - Biopython at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>