[BioPython] ClustalW Multiple Alignment

[Peter]

On Sun, Nov 23, 2008 at 1:21 PM,  <lueck at ipk-gatersleben.de> wrote:
> Hi!
>
> I want to align several sequences under the allowance to check whether there
> are reversed complement.
>
> That means I align all sequences against a reference sequence and then
> reversed complement them and align them again. After that I want to compare
> the score and choose the better once.

If I have understood you correctly, you have one reference nucleotide
sequence, and many nucleotide sequences of unknown orientation.  For
each sequence you want to do a pairwise alignment against the
reference to decide which orientation matches best (forwards, or
reverse complement).

So you want to lots of pairwise alignments.  Perhaps ClustalW is not
the best choice - maybe use EMBOSS needle?  You could also try
Biopython's Bio.pairwise2 module.

> Now my question:
>
> How can I get the score?

What score exactly are you looking for?

> Unfortunately it's not in the dnd file.

The dnd file from clustalw is just a tree, there is no score.

> In an old message of this mailing list, it's was written that it's
> in the log file. Does this has been removed?

What log file?  I didn't think clustalw wrote a log file.  It could be
in the standard output printed to screen...

What old message on the mailing list are you refering to?  Could you
link to it in the archive maybe?
http://lists.open-bio.org/pipermail/biopython/

Peter