[Chimera-users] chimera multiple sequence alignment

Covell, David (NIH/NCI) [E] CovellD at mail.nih.gov
Wed Nov 13 12:20:23 PST 2013

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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