As should be obvious, I sent previous message out before seeing this.  It
appears your original measure IS symmetric, but I did NOT expect negative
off-diagonal measures.  I have no idea what meaning of these negative values
is, and won't try to figure this out right now (no time).  First measure I
suggested could still be used, but I have no idea whether it is appropriate
to this situation or not.

Doug Carroll.

At 12:40 PM 05/02/2001 -0500, William Shannon wrote:
>As a follow-up to my previous email the first 5 rows,columns of the score
matrix
> are:
>
>> blosum62[1:5,1:5]
>   A  R  N  D  C
>A  4 -1 -2 -2  0
>R -1  5  0 -2 -3
>N -2  0  6  1 -3
>D -2 -2  1  6 -3
>C  0 -3 -3 -3  9
>
>
>Comparing sequences ARN to ADC gives similarity scores:
>
>        (s_AA = 4) + (s_RD = -2) + (s_NC = -3) = -1
>
>and ARN to itself
>
>        (s_AA = 4) + (s_RR = 5) + (s_NN = 6) = 15
>
>and ADC to itself
>
>        (s_AA = 4) + (s_DD = 6) + (s_CC = 9) = 19
>
>so the similarity matrix is
>
>        15  -1
>        -1  19
>
>
>--
>
>William D. Shannon, Ph.D.
>
>Assistant Professor of Biostatistics in Medicine
>Division of General Medical Sciences and Biostatistics
>
>Washington University School of Medicine
>Campus Box 8005, 660 S. Euclid
>St. Louis, MO   63110
>
>Phone: 314-454-8356
>Fax: 314-454-5113
>e-mail: [log in to unmask]
>web page: http://ilya.wustl.edu/~shannon
>
>


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