[Biopython] Pairwise alignment - is it a generic function?

[Peter Cock]

On Wed, Oct 26, 2011 at 11:30 AM, João Rodrigues <anaryin at gmail.com> wrote:
> Hello all,
>
> A friend of mine was interested in a small simple alignment script for
> aminoacids, to which I recommended to have a look at Biopython. We found the
> pairwise2 module but we're a bit puzzled. Does it align "any" sequence, aa
> or nucleotides? I don't see any scoring matrix referenced there..

It should work on proteins, just pass in the appropriate scoring matrix.

> Related to this, can you suggest any implementation of an aminoacid
> pairwise alignment algorithm, in Python, that does is self contained
> (ie. doesn't depend on some other program).

Well, Bio.pairwise2 has a faster C implementation and fall back slower
pure Python implementation (used under Jython/PyPy/etc), which might
answer your needs.

Peter