Table 3 Final amino acid substitution matrix optimized for the LA kernel (β = 0:5). Optimization was started from the BLOSUM62 matrix with gap open and extension penalties initialized to 12 and 2 using all the COG distant data. After the optimization procedure, the gap open and extension penalties are 11.6 and 5.7, respectively.
From: Optimizing amino acid substitution matrices with a local alignment kernel
A | 3.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
R | -1.4 | 4.5 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
N | -1.5 | 0.1 | 5.9 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
D | -1.8 | -1.8 | 1.9 | 6.0 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
C | 0.3 | -2.9 | -3.0 | -3.0 | 8.7 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
Q | -0.5 | 1.5 | 0.4 | -0.4 | -3.1 | 4.7 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
E | -1.3 | 0.2 | -0.3 | 2.3 | -4.0 | 2.1 | 3.2 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
G | 0.6 | -2.6 | 0.6 | -0.5 | -3.0 | -1.9 | -1.7 | 6.9 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
H | -2.0 | 0.3 | 0.8 | -0.9 | -3.0 | 0.3 | -0.0 | -1.7 | 8.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
I | -1.5 | -3.0 | -3.3 | -3.3 | -0.8 | -2.6 | -3.4 | -3.9 | -3.0 | 3.5 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
L | -0.5 | -2.3 | -3.3 | -4.4 | -1.2 | -1.9 | -2.6 | -4.0 | -2.9 | 2.7 | 3.6 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
K | -1.0 | 3.7 | 0.5 | -0.3 | -3.1 | 0.8 | 0.0 | -1.5 | -0.7 | -3.0 | -1.9 | 4.0 | Â | Â | Â | Â | Â | Â | Â | Â |
M | -0.5 | -0.9 | -2.1 | -3.0 | -0.9 | 0.3 | -2.2 | -3.1 | -2.0 | 1.5 | 2.5 | -1.3 | 4.8 | Â | Â | Â | Â | Â | Â | Â |
F | -1.3 | -2.5 | -3.0 | -2.8 | -1.9 | -2.9 | -3.3 | -3.2 | -1.2 | 0.3 | 1.0 | -3.0 | 0.2 | 5.2 | Â | Â | Â | Â | Â | Â |
P | -1.0 | -2.3 | -1.9 | -0.4 | -3.1 | -1.2 | -1.2 | -2.1 | -2.0 | -3.1 | -2.5 | -1.0 | -1.9 | -4.1 | 7.7 | Â | Â | Â | Â | Â |
S | 2.2 | -0.9 | 0.6 | -0.1 | -1.0 | 0.8 | 0.0 | 0.5 | -0.8 | -1.9 | -2.4 | 0.1 | -1.4 | -1.8 | -0.7 | 4.0 | Â | Â | Â | Â |
T | 1.0 | -0.5 | 0.0 | -0.7 | -1.2 | -0.7 | -0.7 | -1.9 | -1.8 | -1.3 | -1.2 | -0.7 | -1.0 | -1.6 | -0.9 | 1.5 | 5.0 | Â | Â | Â |
W | -3.1 | -3.0 | -4.1 | -4.0 | -1.9 | -1.9 | -2.9 | -1.9 | -1.9 | -2.8 | -1.8 | -2.9 | -1.2 | 0.7 | -4.0 | -3.1 | -2.0 | 10.5 | Â | Â |
Y | -1.8 | -1.6 | -1.8 | -3.1 | -2.0 | -1.0 | -2.2 | -3.5 | 2.3 | -1.0 | -0.9 | -2.4 | -0.8 | 2.8 | -3.3 | -1.9 | -2.0 | 2.4 | 6.3 | Â |
V | 0.5 | -2.8 | -2.6 | -3.7 | -0.7 | -1.9 | -1.9 | -3.1 | -3.1 | 4.0 | 1.2 | -2.1 | 1.4 | -0.4 | -1.9 | -2.3 | 0.2 | -2.8 | -1.0 | 3.9 |
| Â | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V |