module Bio.Sequence.Alignment.Matrix
( ScoringMatrix (..)
, BLOSUM62 (..), PAM250 (..), NUC44 (..)
, blosum62, pam250, nuc44
, matrix
) where
import Bio.Sequence.Alignment.Internal.Matrix.Scoring
import Bio.Sequence.Alignment.Internal.Matrix.Template
[matrix|BLOSUM62
# Matrix made by matblas from blosum62.iij
# * column uses minimum score
# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
# Blocks Database = /data/blocks_5.0/blocks.dat
# Cluster Percentage: >= 62
# Entropy = 0.6979, Expected = -0.5209
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 1 2 2 0 1 1 0 2 1 1 1 1 2 1 1 0 3 2 0 2 1 0 4
R 1 5 0 2 3 1 0 2 0 3 2 2 1 3 2 1 1 3 2 3 1 0 1 4
N 2 0 6 1 3 0 0 0 1 3 3 0 2 3 2 1 0 4 2 3 3 0 1 4
D 2 2 1 6 3 0 2 1 1 3 4 1 3 3 1 0 1 4 3 3 4 1 1 4
C 0 3 3 3 9 3 4 3 3 1 1 3 1 2 3 1 1 2 2 1 3 3 2 4
Q 1 1 0 0 3 5 2 2 0 3 2 1 0 3 1 0 1 2 1 2 0 3 1 4
E 1 0 0 2 4 2 5 2 0 3 3 1 2 3 1 0 1 3 2 2 1 4 1 4
G 0 2 0 1 3 2 2 6 2 4 4 2 3 3 2 0 2 2 3 3 1 2 1 4
H 2 0 1 1 3 0 0 2 8 3 3 1 2 1 2 1 2 2 2 3 0 0 1 4
I 1 3 3 3 1 3 3 4 3 4 2 3 1 0 3 2 1 3 1 3 3 3 1 4
L 1 2 3 4 1 2 3 4 3 2 4 2 2 0 3 2 1 2 1 1 4 3 1 4
K 1 2 0 1 3 1 1 2 1 3 2 5 1 3 1 0 1 3 2 2 0 1 1 4
M 1 1 2 3 1 0 2 3 2 1 2 1 5 0 2 1 1 1 1 1 3 1 1 4
F 2 3 3 3 2 3 3 3 1 0 0 3 0 6 4 2 2 1 3 1 3 3 1 4
P 1 2 2 1 3 1 1 2 2 3 3 1 2 4 7 1 1 4 3 2 2 1 2 4
S 1 1 1 0 1 0 0 0 1 2 2 0 1 2 1 4 1 3 2 2 0 0 0 4
T 0 1 0 1 1 1 1 2 2 1 1 1 1 2 1 1 5 2 2 0 1 1 0 4
W 3 3 4 4 2 2 3 2 2 3 2 3 1 1 4 3 2 11 2 3 4 3 2 4
Y 2 2 2 3 2 1 2 3 2 1 1 2 1 3 3 2 2 2 7 1 3 2 1 4
V 0 3 3 3 1 2 2 3 3 3 1 2 1 1 2 2 0 3 1 4 3 2 1 4
B 2 1 3 4 3 0 1 1 0 3 4 0 3 3 2 0 1 4 3 3 4 1 1 4
Z 1 0 0 1 3 3 4 2 0 3 3 1 1 3 1 0 1 3 2 2 1 4 1 4
X 0 1 1 1 2 1 1 1 1 1 1 1 1 1 2 0 0 2 1 1 1 1 1 4
* 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 1
|]
[matrix|PAM250
#
# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
#
# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
#
# Expected score = -0.844, Entropy = 0.354 bits
#
# Lowest score = -8, Highest score = 17
#
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 2 2 0 0 2 0 0 1 1 1 2 1 1 3 1 1 1 6 3 0 0 0 0 8
R 2 6 0 1 4 1 1 3 2 2 3 3 0 4 0 0 1 2 4 2 1 0 1 8
N 0 0 2 2 4 1 1 0 2 2 3 1 2 3 0 1 0 4 2 2 2 1 0 8
D 0 1 2 4 5 2 3 1 1 2 4 0 3 6 1 0 0 7 4 2 3 3 1 8
C 2 4 4 5 12 5 5 3 3 2 6 5 5 4 3 0 2 8 0 2 4 5 3 8
Q 0 1 1 2 5 4 2 1 3 2 2 1 1 5 0 1 1 5 4 2 1 3 1 8
E 0 1 1 3 5 2 4 0 1 2 3 0 2 5 1 0 0 7 4 2 3 3 1 8
G 1 3 0 1 3 1 0 5 2 3 4 2 3 5 0 1 0 7 5 1 0 0 1 8
H 1 2 2 1 3 3 1 2 6 2 2 0 2 2 0 1 1 3 0 2 1 2 1 8
I 1 2 2 2 2 2 2 3 2 5 2 2 2 1 2 1 0 5 1 4 2 2 1 8
L 2 3 3 4 6 2 3 4 2 2 6 3 4 2 3 3 2 2 1 2 3 3 1 8
K 1 3 1 0 5 1 0 2 0 2 3 5 0 5 1 0 0 3 4 2 1 0 1 8
M 1 0 2 3 5 1 2 3 2 2 4 0 6 0 2 2 1 4 2 2 2 2 1 8
F 3 4 3 6 4 5 5 5 2 1 2 5 0 9 5 3 3 0 7 1 4 5 2 8
P 1 0 0 1 3 0 1 0 0 2 3 1 2 5 6 1 0 6 5 1 1 0 1 8
S 1 0 1 0 0 1 0 1 1 1 3 0 2 3 1 2 1 2 3 1 0 0 0 8
T 1 1 0 0 2 1 0 0 1 0 2 0 1 3 0 1 3 5 3 0 0 1 0 8
W 6 2 4 7 8 5 7 7 3 5 2 3 4 0 6 2 5 17 0 6 5 6 4 8
Y 3 4 2 4 0 4 4 5 0 1 1 4 2 7 5 3 3 0 10 2 3 4 2 8
V 0 2 2 2 2 2 2 1 2 4 2 2 2 1 1 1 0 6 2 4 2 2 1 8
B 0 1 2 3 4 1 3 0 1 2 3 1 2 4 1 0 0 5 3 2 3 2 1 8
Z 0 0 1 3 5 3 3 0 2 2 3 0 2 5 0 0 1 6 4 2 2 3 1 8
X 0 1 0 1 3 1 1 1 1 1 1 1 1 2 1 0 0 4 2 1 1 1 1 8
* 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1
|]
[matrix|NUC44
#
# This matrix was created by Todd Lowe 12/10/92
#
# Uses ambiguous nucleotide codes, probabilities rounded to
# nearest integer
#
# Lowest score = -4, Highest score = 5
#
A T G C S W R Y K M B V H D N
A 5 4 4 4 4 1 1 4 4 1 4 1 1 1 2
T 4 5 4 4 4 1 4 1 1 4 1 4 1 1 2
G 4 4 5 4 1 4 1 4 1 4 1 1 4 1 2
C 4 4 4 5 1 4 4 1 4 1 1 1 1 4 2
S 4 4 1 1 1 4 2 2 2 2 1 1 3 3 1
W 1 1 4 4 4 1 2 2 2 2 3 3 1 1 1
R 1 4 1 4 2 2 1 4 2 2 3 1 3 1 1
Y 4 1 4 1 2 2 4 1 2 2 1 3 1 3 1
K 4 1 1 4 2 2 2 2 1 4 1 3 3 1 1
M 1 4 4 1 2 2 2 2 4 1 3 1 1 3 1
B 4 1 1 1 1 3 3 1 1 3 1 2 2 2 1
V 1 4 1 1 1 3 1 3 3 1 2 1 2 2 1
H 1 1 4 1 3 1 3 1 3 1 2 2 1 2 1
D 1 1 1 4 3 1 1 3 1 3 2 2 2 1 1
N 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1
|]