I am interested in calculating the homology scores obtained from a set of
aligned protein sequences. In particular I want to estimate the expected scores
from a database of similar composition but of random sequence. This seems
fairly straightforward when identical amino acids are considered, but is more
problematical when the Dayhoff substitution matrix is used to calculate a
"conserved" replacement score. I am sure that this problem has been considered
before and I would be very grateful to anybody who could either direct me to a
source or make some suggestions.
Many thanks
Craig Marshall bioc07 at otago.ac.nz
Department of Biochemistry Tel +64 3 479 7871
University of Otago Fax +64 3 479 7866
P.O. Box 56
Dunedin
New Zealand
