[Biopython] "Appending" to an MSA

[Ivan Gregoretti]

Hello Eric,

The functionality you are looking for does not exist in Biopython. Yet, as
Peter suggests, there is command line hope for you:

Clustal Omega
http://www.clustal.org/omega/

Specifically, see the documentation where it tells you how to align one or
more sequences against a profile of pre-aligned sequences.

Notice that nothing prevents you from running Clustal Omega as a subprocess
from within Python. Actually, it works very well and you can read in its
output from a PIPE using SeqIO.parse(...,'fasta').

I hope this helps,

Ivan


Ivan Gregoretti, PhD
Bioinformatics



On Mon, Jul 29, 2013 at 6:53 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Monday, July 29, 2013, Eric Ma wrote:
>
> > Many apologies if this sounds like a dumb question, but I'm kinda stuck
> > here. I've posted on StackOverflow and BioStars, but haven't received an
> > answer, so I'm going to cross-post my question below.
> >
> >
> Links? I don't see it here - maybe you didn't tag the question?
> http://www.biostars.org/show/tag/biopython/
>
> Here's the duplicate on SO:
>
> http://stackoverflow.com/questions/17911075/multiple-sequence-alignment-appending-to-an-alignment
>
>
> > I have a set of 520 influenza sequences for which I have already done
> > multiple sequence alignment, and computed the pairwise identity matrix.
> If
> > I'd like to add in another sequence, I have to re-align everything, and
> > recompute the entire PWI matrix. Is there any program I can use to
> "append"
> > this other sequence to the alignment, and only compute the PWI w.r.t.
> every
> > other sequence?
>
>
> I think some command line tools will do that, but it may give a
> different answer to a fresh alignment - and therefore could be
> a bad idea for many downstream analyses...
>
> Are you hoping for advice for how to implement this yourself
> in (bio)python?
>
> Peter
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