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Table 1 Amino acid substitution matrix optimized for the SW score. Optimization was started from the BLOSUM62 matrix with gap open and extension penalties initialized to 12 and 2 respectively, on COG training data. After the optimization procedure, the open and extension penalties are 12.3 and 2.8, respectively.

From: Optimizing amino acid substitution matrices with a local alignment kernel

A

4.5

                   

R

-0.9

5.2

                  

N

-1.9

0.1

5.9

                 

D

-2.0

-2.0

1.2

6.2

                

C

0.1

-3.0

-3.0

-3.0

9.0

               

Q

-0.9

1.0

0.0

0.1

-3.0

5.1

              

E

-0.8

0.1

0.1

2.1

-4.0

2.1

5.0

             

G

0.2

-2.0

0.1

-0.9

-3.0

-1.9

-1.8

6.3

            

H

-2.0

0.0

1.1

-1.0

-3.0

-0.0

0.1

-2.0

8.0

           

I

-0.8

-2.9

-3.0

-3.1

-1.0

-3.0

-3.1

-3.9

-3.0

4.0

          

L

-0.8

-1.9

-3.0

-4.0

-1.0

-2.0

-2.9

-3.9

-3.0

2.6

4.4

         

K

-0.8

2.3

0.0

-1.0

-3.0

1.2

1.1

-2.0

-0.9

-3.0

-1.9

4.8

        

M

-1.0

-1.0

-2.0

-3.0

-1.0

0.0

-2.0

-3.0

-2.0

1.2

2.1

-1.0

5.0

       

F

-1.9

-2.9

-3.0

-3.0

-2.0

-3.0

-3.0

-3.0

-1.0

0.2

0.3

-3.0

0.0

6.1

      

P

-1.0

-2.0

-2.0

-0.9

-3.0

-1.0

-1.0

-1.9

-2.0

-3.0

-2.9

-1.0

-2.0

-4.0

7.1

     

S

1.3

-1.0

1.1

0.1

-1.0

0.1

0.1

0.2

-1.0

-1.9

-1.9

-0.0

-1.0

-1.9

-0.9

4.0

    

T

0.2

-1.0

0.1

-1.0

-1.0

-0.9

-0.9

-1.9

-2.0

-0.9

-0.8

-1.0

-1.0

-1.9

-1.0

1.1

5.1

   

W

-3.0

-3.0

-4.0

-4.0

-2.0

-2.0

-3.0

-2.0

-2.0

-3.0

-1.9

-3.0

-1.0

1.0

-4.0

-3.0

-2.0

11.1

  

Y

-1.9

-1.9

-2.0

-3.0

-2.0

-0.9

-2.0

-3.0

2.1

-1.0

-0.8

-2.0

-1.0

3.2

-3.0

-2.0

-2.0

2.0

7.0

 

V

0.2

-3.0

-3.0

-3.0

-1.0

-2.0

-2.0

-3.0

-3.0

3.4

1.2

-2.0

1.1

-0.9

-1.9

-1.9

0.1

-3.0

-1.0

4.2

 

A

R

N

D

C

Q

E

G

H

I

L

K

M

F

P

S

T

W

Y

V