[Chimera-users] Adding sequences to an alignment

Tom Goddard goddard at sonic.net
Wed Nov 2 17:53:47 PDT 2011

Hi David,

   Here's the documentation on adding sequences to an alignment in Chimera


It says it uses the Needleman-Wunsch algorithm with parameters you 
specify unless you have the "Simply append..." option enabled in which 
case it puts the sequence at the bottom with no gaps if the sequence has 
exactly the same length as the existing alignment.  I guess you don't 
have Simply Append enabled.  Probably Needleman-Wunsch is simply failing 
to align your new sequence to the existing alignment so it ends up 
putting it to the right of the existing alignment my inserting a huge 
gap at the beginning.

   How similar is the sequence you are trying to add to the alignment 

   I'm not the Chimera expert on this topic  (Eric Pettersen and Elaine 
Meng are) so I've posted to the Chimera mailing list so they can give 
you a better answer.


> Hi Tom,
> My name is David and I'm a postdoc in Jack Johnson lab at Scripps. I'm writing as I've a question concerning the use of Chimera.
> I've superimposed two structures in Chimera and generated a structure-based sequence alignement. I have two set of sequences (2 families) with a group associated with one of the two structures (and thus its sequence) and the other group being linked to the second structure.
> I tried to extend the structure based sequence-alignement by adding new sequences and adding the first 2 sequences exactly did that i wanted: aligning them to the corresponding reference whose structure is displayed.
> However when I add the other group of sequence, it doesn't result in aligning to the other sequence and instead add it after the overall alignment.
> I'm sure that I'm missing something obvious, could you please help me sorting that out?
> Thanks a lot
> Best wishes
> David
> David Veesler
> Research Associate
> The structural Virology lab - Johnson's lab
> Department of Molecular Biology
> The Scripps Research Institute
> 10550, N. Torrey Pines Road
> La Jolla, California 92037, USA

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