Scoring aligned sequences

bioc07 at otago.ac.nz bioc07 at otago.ac.nz
Sat Mar 7 04:24:22 EST 1992

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
New Zealand

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