1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
|
/////////////////////////////////////////////////////////////////
// Matrix.h
//
// Specifies scoring matrices and their structure
//
//
//
/////////////////////////////////////////////////////////////////
typedef struct{
char monomers[26]; /* amino or nucleic acid order */
float matrix[676]; /* entries of the score matix, 26*26=676 */
} score_matrix;
//default protein sequence scoring matrix as well as default scoring matrix of the PROBALIGN
//also used when -prot option is used
score_matrix gonnet_160 =
{
"ABCDEFGHIKLMNPQRSTVWXYZ",
{ 4.6,
0.0, 0.0,
0.3, 0.0, 13.5,
-1.1, 0.0, -5.3, 7.0,
-0.4, 0.0, -5.2, 3.4, 5.9,
-3.8, 0.0, -1.8, -7.0, -6.2, 9.1,
0.2, 0.0, -3.4, -0.7, -2.1, -7.6, 8.2,
-1.8, 0.0, -2.3, -0.1, -0.1, -0.7, -2.7, 9.3,
-1.8, 0.0, -2.5, -6.2, -4.3, 0.3, -7.0, -3.7, 5.9,
-1.2, 0.0, -4.8, -0.1, 1.3, -5.3, -2.4, 0.2, -3.5, 5.5,
-2.2, 0.0, -2.9, -6.5, -4.5, 1.9, -6.7, -3.2, 3.0, -3.4, 5.7,
-1.2, 0.0, -1.9, -5.0, -3.1, 1.4, -5.2, -2.1, 2.9, -2.1, 3.4, 7.6,
-1.2, 0.0, -3.1, 2.6, 0.5, -4.7, -0.2, 1.5, -4.4, 0.8, -4.8, -3.6, 6.5,
-0.1, 0.0, -5.2, -1.9, -1.4, -5.8, -3.0, -2.2, -4.3, -1.6, -3.5, -4.2, -2.2, 9.6,
-0.7, 0.0, -4.2, 0.6, 2.3, -4.1, -2.1, 1.7, -3.2, 2.0, -2.4, -1.2, 0.5, -0.8, 5.6,
-1.6, 0.0, -3.5, -1.6, -0.3, -5.3, -2.1, 0.3, -4.1, 3.5, -3.5, -2.9, -0.4, -2.1, 1.7, 7.1,
1.6, 0.0, -0.2, 0.0, -0.3, -4.5, -0.1, -0.8, -3.3, -0.4, -3.6, -2.3, 1.1, 0.0, -0.2, -0.9, 4.4,
0.5, 0.0, -1.4, -0.6, -0.8, -3.6, -2.4, -0.8, -1.2, -0.2, -2.4, -1.1, 0.3, -0.4, -0.4, -0.9, 2.3, 5.0,
0.1, 0.0, -0.6, -4.9, -3.0, -0.8, -5.2, -3.5, 4.0, -3.0, 1.7, 1.4, -3.8, -3.2, -2.7, -3.4, -2.0, 0.0, 5.3,
-5.5, 0.0, -2.1, -7.8, -6.4, 3.2, -5.5, -1.9, -3.4, -5.4, -2.0, -2.2, -5.5, -7.4, -4.0, -2.4, -4.7, -5.4, -4.5, 15.8,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-3.7, 0.0, -1.3, -4.2, -4.4, 5.6, -6.0, 2.7, -2.0, -3.5, -1.1, -1.3, -2.2, -4.8, -2.9, -2.9, -2.8, -3.2, -2.4, 3.8, 0.0, 10.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
}
};
//default nucleotide sequence scoring matrix
//used when -nuc option is used
score_matrix nuc_simple=
{
"ABCDGHKMNRSTUVWXY",
/*
{
1,
0, 0,
0, 0, 1,
0, 0, 0, 0,
0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
}
*/
{
5,
0, 0,
-4, 0, 5,
0, 0, 0, 0,
-4, 0, -4, 0, 5,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-4, 0, -4, 0, -4, 0, 0, 0, 0, 0, 0, 5,
-4, 0, -4, 0, -4, 0, 0, 0, 0, 0, 0, 5, 5,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
}
//Ribosum85-60
/*
{
2.22,
0, 0,
-1.86, 0, 1.16,
0, 0, 0, 0,
-1.46, 0, -2.48, 0, 1.03,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-1.39, 0, -1.05, 0, -1.74, 0, 0, 0, 0, 0, 0, 1.65,
-1.39, 0, -1.05, 0, -1.74, 0, 0, 0, 0, 0, 0, 0, 1.65,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
}
*/
};
|
