[Chimera-users] search for the conserved domain alignment algorithm

Elaine Meng meng at cgl.ucsf.edu
Mon May 12 15:37:12 PDT 2014

Hi XY,
No -- if I understand correctly, the CDD has sequence alignments imported from outside sources (other databases) as well as human-curated alignments. 

I wasn't sure whether you meant sequence alignment or 3D structure alignment, but you can save the CDD sequence alignment as a file and then open it in Chimera.  You could also open the structures and then tell Chimera to superimpose the structures using the CDD sequence alignment.

For example, if I go to this page with a curated CDD sequence alignment:

… I can go down to the Sequence Alignment section, choose format mFasta, click Reformat,  then copy and paste into a plain text file named (for example) cdd.fa, attached.  I can see that there are some structure sequences in the alignment, including 2ax9, 1xj7, 1t73, ...

In Chimera, I can open cdd.fa and PDBs 2zx9, 1xj7, 1t73.  In the sequence window menu: Structure… Match will bring up a dialog for superimposing the structures using the sequence alignment.
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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On May 10, 2014, at 4:56 AM, ce <allderann at gmail.com> wrote:

> Hi,
> Does Chimera constain an algorithm that can generateconserved domain alignment in the exact way as Entrez CDD alignment works ?
> Yours sincerelly,
> XY

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