Biomedical Engineering Reference
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I -1 -2 -2 -2 -2 -2 -2 -3 -2 5
L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6
K -1 3 1 0 -5 1 0 -2 0 -2 -3 5
M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6
F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9
P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6
S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2
T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3
W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17
Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10
V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4
B 0 -1 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 -1 0 0 -5 -3 -2 2
Z 0 0 1 3 -5 3 3 -1 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3
X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Although the values in the Blosum matrix mean the same as in a PAM matrix, the Blosum matrices
incorporate substitution scores that encompass a range of evolutionary periods and in some cases
provide greater sensitivity over PAM matrices. Blosum takes its name from the blocks—areas of
conserved amino acids—used to define substitution patterns. Unlike PAM, which is based on a
relatively small set of closely related proteins, Blosum is based on a large-scale analysis of over 500
families of related proteins. Similarly, Blosum doesn't explicitly consider evolutionary factors.
Matrices aren't necessarily symmetric or based on the same alphabet. For example, it's possible to
relate polypeptides to experimental or environmental conditions. Furthermore, although this
discussion of matrices has centered on polypeptides, they can also be designed for use with nucleic
acids. The matrix values of these matrices are necessarily different from those used with
polypeptides.
Figure 8-6 The Blocks Amino Acid Substitution Matrix 62 (Blosum62).
BLOSUM62 SUBSTITUTION MATRIX
A R N D C Q E G H I L K M F P S T W Y V B Z X
A 4
R -1 5
N -2 0 6
D -2 -2 1 6
C 0 -3 -3 -3 9
Q -1 1 0 0 -3 5
E -1 0 0 2 -4 2 5
G 0 -2 0 -1 -3 -2 -2 6
