[Biopython] "Appending" to an MSA

[Eric Ma]

Many thanks! I think I will try aligning new sequences against the old
profile of pre-aligned sequences, to see if I can get that desired output.

Cheers,
Eric
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On Tue, Jul 30, 2013 at 8:56 AM, Ivan Gregoretti <ivangreg at gmail.com> wrote:

> 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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>>
>
>