[BioPython] ClustalW Multiple Alignment

[Stefanie Lück]

Yes, first I want to make a pairwise alignment to find the right orientation 
of all sequences and after it's I'll align everything in a multiple 
alignment.

I meant this message:
http://lists.open-bio.org/pipermail/biopython/2005-May/002656.html

So you're right they talk about the printed output.
I try to get the score.
Thanks for the link!
Stefanie

----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: <lueck at ipk-gatersleben.de>
Cc: <biopython at lists.open-bio.org>
Sent: Sunday, November 23, 2008 2:32 PM
Subject: Re: [BioPython] ClustalW Multiple Alignment


> 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
>