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Dear Donghui,
even within one program (clustalw) you would get different results by
picking different weighting schemes (clustalx: Aligment->Alignment
Parameter -> Multiple Alignment Parameter: BLOSUM, PAM, Gonnet...).
As with any software I would assume the developers know best what they
are doing and recommend to stick to the defaults unless you know what
you are doing.
Regards,
Tim
On 05/15/12 08:02, wu donghui wrote:
> Dear all,
>
> I want to know your suggestions about current protein sequence
> alignment programs. It seems that different programs give different
> alignment results such as from analysis of Clustal W and MULTALIN.
> Thanks for any input or comments.
>
> Best regards,
>
> Donghui
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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