Algorithms on Sequences

Identity and default Blast Matrices
A 3
A
T
C
G
A T C G
1
0
0
0
0 0 0
1
0
0
0 0
1
0
0
1
A T C G
Identity matrix Reference matrix in BLAST
A
T
C
G
5
-4 -4 -4
5
-4 -4
Matrix based on the genetic code
A R N D C Q E G H I L K M F P S T W Y V
R 1 3
N 1 1 3
D 2 1 2 3
C 1 2 1 1 3
Q 1 2 1 1 0 3
E 2 1 1 2 0 2 3
G 2 2 1 2 2 1 2 3
H 1 2 2 2 1 2 1 1 3
I 1 2 2 1 1 1 1 1 1 3
L 1 2 1 1 1 2 1 1 2 2 3
K 1 2 2 1 0 2 2 1 1 2 1 3
M 1 2 1 0 0 1 1 1 0 2 2 2 3
F 1 1 1 1 2 0 0 1 1 2 2 0 1 3
P 2 2 1 1 1 2 1 1 2 1 2 1 1 1 3
S 2 2 2 1 2 1 1 2 1 2 2 1 1 2 2 3
T 2 2 2 1 1 1 1 1 1 2 1 2 2 1 2 2 3
W 1 2 0 0 2 1 1 2 0 0 2 1 1 1 1 2 1 3
Y 1 1 2 2 2 1 1 1 2 1 1 1 0 2 1 2 1 1 3
V 2 1 1 2 1 1 2 2 1 2 2 1 2 2 1 1 1 1 1 3
-4
-4
-4
-4
-4
5
-4
-4
5
(number of
modifications
to pass from
an amino acid
to another)