[Chimera-users] Adding sequences to an alignment

[Elaine Meng]

Hi David,
In Chimera, you could try repeatedly removing the sequences that don't align well and adding them back again with different alignment parameter settings.  However, if the sequences are hard to align (fairly dissimilar from what's already in your alignment) that admittedly tedious approach may not be successful and you may need to either resort to manual editing, also rather tedious, or trying some other combination of methods which may or may not include Chimera.  Chimera allows some alignment editing, but if you are going to do a lot of manual editing, there are other programs mainly intended for that purpose that may be more facile.

Chimera Multalign Viewer docs, see "editing and saving" section:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

I know some people have used Chimera Matchmaker and Match->Align to generate the structure-based sequence alignment of representative structures, but then used another alignment-editing program to manually collate their alignments of the separate sequence groups, guided by that structure-based alignment.  I don't remember which other programs were used, however.

I believe there are some methods that will try to collate your input alignments (group 1 alignment, group 2 alignment, structure-based sequence alignment from Chimera of representatives from both groups) with as little disruption as possible into one bigger multiple sequence alignment, but I haven't done that myself.  For example, "T-Coffee Combine" server:
<http://tcoffee.crg.cat/apps/tcoffee/play?name=combine>

There are also methods that use both structure and sequence information in creating multiple alignments.  Again, I haven't done this for my own research, only read about the methods in papers.  For example, "PROMALS3D" server:
<http://prodata.swmed.edu/promals3d/promals3d.php>

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

On Nov 2, 2011, at 5:53 PM, Tom Goddard wrote:

> Hi David,
> 
>   Here's the documentation on adding sequences to an alignment in Chimera
> 
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#add
> 
> 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 
> sequences?
> 
>   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.
> 
>     Tom
> 
> 
>> 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
>>