[BioPython] Clustalw pair wise alignment

[Peter]

Hi Stefanie

> I working with clustalw and everything works fine. No I have some questions:
>
> 1) Must the input data be in a file or can it also be in the code (e.g. in a list)?

I believe for the Clustalw command line tool, you have to supply the
input data in a file.

> 2) Because, I want to do many (up to hundreds) pair wise
> alignments (short sequences) and I don't want to store
> each of them in a separate file.
>
> If I have it in one file, clustalw make a multiple alignment:

Yes, that is expected for clustalw.

> Could someone give a hint?

If you want to use Clustalw, you could re-use a temporary file for
each pair of sequences (rather than creating hundreds of different
input files).

I would consider using the EMBOSS tools "needle" or "water" for doing
pairwise alignments.  These have the advantage that you can actually
supply the sequence as part of the command line (provided they are not
too long).  See http://emboss.sourceforge.net/apps/ and also
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html#asis

Peter