[Chimera-users] chimera multiple sequence alignment

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 13 13:51:37 PST 2013

Dear David,
You can get all-by-all percent identities by choosing "all sequences" from each pulldown menu in the percent identity dialog.  It probably wasn't obvious because these appear at the bottom of each menu and you had a large number of sequences.  Maybe we should put that choice at the top of the menus instead! The results would go to the Reply Log (under Favorites in the menu) and can be saved to a text file from there.

Identity is simply identity, the percentage of positions with the exact same residue type; the calculation does not use a scoring matrix.  Chimera doesn't have an option to score an existing alignment.  It does produce a score using your chosen matrix when you use Chimera to add a sequence to the alignment (sequence window menu: Edit... Add Sequence) but it is not a pairwise score unless you use only one of the sequences in the  existing alignment as the "Guide for aligning" the new one.

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

On Nov 13, 2013, at 12:20 PM, Covell, David (NIH/NCI) [E] wrote:

> Dear Chimera Help,
> I have used NCBI’s COBALT to align the active site residues for the ~400 kinases in the ‘kinome tree’. This fasta alignment can be exported and read into chimera. 
> Once loaded,
> tools  >  sequence  >  multialign/viewer > info > percent identity
> gives me the % identity for a pair of sequences. Since I have ~400 sequences, I would like to know whether the upper-triangular matrix of percent identities can be done automatically. If so, can a weight matrix for scoring (BLOSUM62) be used?
> Thanks in advance for your help.
> David Covell, Ph.D.

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