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