I am trying to work out the replacement/substitution ratios in the
CDR and FR regions of some human autoantibody sequences. The problem
is how to score a situation where two or three bases in a codon for a
given amino acid are changed. Is it normal practice to consider each
mutation separately for the effect it would have had if the other
bases were in germline configuration? Or can you try to score on a
single codon basis? If you are using these figures as an index of
antigen-driven selection then the approach used is important as the
values will be different and the former contains assumptions about
the order of mutations which is unknown.
Any comments or have I missed something?
Mark Hexham
Sheffield UK
