[Chimera-users] Question about adding a sequence to a previous structural alignment...

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 18 09:15:51 PDT 2009

Hi Sergio,
If I understand correctly, you used "Edit... Add Sequence" in  
Multalign Viewer to add another sequence to the alignment output by  
Match->Align.  That does not change the 3D structural alignment (how  
the structures are matched), and it also does not change the multiple  
sequence alignment from Match->Align except that additional gap  
columns may be inserted between the columns that were already there.   
In other words, there may be places where the new sequence has a  
residue but the sequences in the original alignment all have a gap  

I recommend saving the Match->Align result in a Chimera session and/or  
as an alignment file, so that you can easily try different parameters  
for adding the new sequence.  It is not possible to tell from % ID  
what the best parameters are... unfortunately it is always case- 
dependent.  I can only recommend trying a few different settings and  
using your knowledge of these proteins and your intuition to decide  
which result is the best.  However, some rough guidelines are that you  
could try the BLOSUM matrix determined for more similar % IDs to your  
situation (e.g. BLOSUM-30), and if you want fewer columns inserted in  
your original alignment, increase the gap penalties.  It may be that  
the new sequence has a loop where the others do not, however, and in  
that case gaps should be inserted.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 18, 2009, at 5:32 AM, Sergio Garay wrote:

> Hi all
> I've prepared an structural alignment of my 3 protein templates  
> using MatchMaker/Match-Align tools.
> The question is: when I add my target sequence to the profile  
> obtained in the step before, Does this
> procedure change my previous structural alignment?, or It just  
> aligns the added sequence to my profile.
> The parameters that I used to add my target sequence are: Blosum-62,  
> gap open, and gap extension
> penalties: 12 and 1 respectively.
> The second problem I have, its not related to chimera, but may be  
> one of you can answer it. My target
> only has 29 % of identical residues with my templates, so Should I  
> use a less stringent parameters to
> make my alignment?
> Any help would be appreciated.

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