What is a good weighting scheme for seqence alignment statistics?

Gerstein M. mbg at mrc-lmb.cam.ac.uk
Mon Jun 14 07:48:58 EST 1993

I have a long sequence alignment of roughly 500 sequences.  I am
calculating a certain property for each sequence (say charge), and I
want to find the mean value and the standard deviation of this property
over all the sequences. All the sequences are aligned with reference
to a key sequence of known structure. Most of the sequences (~300)
have high homology (~80%) to the key sequence and the remainder have
low homology (~20%). I want to compute statistics that weight the
low homology sequences higher.  I thought of weighting each sequence
in the average by 1/(homology^2).

Is there a better weighting scheme? If it is published, what is the
appropriate literature reference.

mark (mbg at mrc-lmb.cam.ac.uk)

AUG-GCU-AGA-AAG                                (INTERNET mbg at mrc-lmb.cam.ac.uk)
M   A   R   K        

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