[ssml] FW: Consesus of Multiple sequence alignment

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Wed Aug 25 03:35:38 EDT 2004

On Tue, 24 Aug 2004, Goel, Manisha wrote:

>>  -----Original Message-----
>> From: 	Goel, Manisha  
>> Sent:	Tuesday, August 24, 2004 2:15 PM
>> To:	'pdb-l at sdsc.edu'
>> Subject:	Consesus of Multiple sequence alignment
>> Hi all,
>> I am new to seq alignments and I am at present using a couple of
>> programs to align my sequences (ClustalX, MUSCLE, T_Cofee)
>> The alignment agrees in most parts but still differs substantially, Is
>> there any automated method of combining the Multiple seq alignment
>> from various sources to get a consensus alignment. Otherwise, I guess,
>> I have to compare all of the outputs to generate one.

I have heard about methods to build 'profiles' from each multiple 
alignment, and then compare the profiles, but this probably isn't what you

Each different alignment program has its own strengths and weeknesses
(not always in equal measure). Your best bet is trying to work out which
program is giving you the most sensible (most stable) alignment.

Try showing your alignments to an expert, or compare them to structural
data, or try to predict secondary structure to validate the 'inserts' in
your alignment. 

Perhaps you can get better results by combining all your data into one
consensus consensus, but I guess you need to properly understand the
components first?

Best of luck!

>> Thanks,
>> - Manisha 

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