prophecy.txt

emboss的linux版本的源代码

.00 0.73 0.30 3.20 4.44 0.86 0.00 -1.40 1.49 0.00 -1.00 0.00 4.55 4.55
5.00 0.00 0.17 0.46 0.82 -0.02 1.95 -0.97 1.80 0.00 0.01 1.97 1.98 0.43 0.00 1.
70 0.09 -1.69 1.93 4.27 0.00 2.35 -2.37 0.00 -1.16 0.00 4.55 4.55
-2.55 0.00 -5.95 -2.39 -2.60 2.54 -3.01 0.83 -2.78 0.00 3.36 0.58 -1.46 2.63 0.
00 -2.83 -0.44 6.18 2.03 -1.52 0.00 -3.89 5.08 0.00 3.02 0.00 4.55 4.55
3.64 0.00 0.44 2.21 1.97 -1.76 3.66 -0.75 3.33 0.00 -0.33 1.62 1.37 0.41 0.00 1
.42 0.65 -1.71 1.00 1.89 0.00 5.44 -6.44 0.00 -2.04 0.00 4.55 4.55
1.26 0.00 -3.44 3.35 4.37 -4.35 1.02 1.47 -1.45 0.00 6.61 -2.18 0.11 2.59 0.00
2.55 3.18 3.52 1.71 1.58 0.00 -1.06 -2.90 0.00 -4.41 0.00 4.55 4.55
5.63 0.00 1.62 -0.17 0.07 -0.23 2.38 -1.35 3.78 0.00 -0.99 2.86 2.17 -0.53 0.00
 1.71 -0.40 -2.30 0.92 1.85 0.00 5.48 -4.58 0.00 -0.57 0.00 4.55 4.55
3.69 0.00 0.50 3.58 2.62 -2.00 2.31 1.96 -0.88 0.00 0.61 -1.50 -1.43 4.77 0.00
0.16 1.47 -1.17 1.34 1.22 0.00 -0.72 -2.56 0.00 0.36 0.00 4.55 4.55
1.44 0.00 0.96 0.44 0.44 -0.70 1.15 -0.32 -0.13 0.00 0.26 -0.58 -0.39 0.51 0.00
 0.83 -0.01 -0.05 2.20 0.64 0.00 -0.01 -0.10 0.00 -0.70 0.00 3.49 3.49
-0.31 0.00 -2.56 -1.23 -0.83 1.74 -0.42 -0.35 1.36 0.00 0.54 2.24 0.38 0.32 0.0
0 -0.98 -0.84 1.99 1.16 1.45 0.00 1.65 -0.65 0.00 1.18 0.00 4.55 4.55
3.32 0.00 1.76 2.69 2.62 -1.00 2.98 0.36 0.29 0.00 -0.22 -0.91 -0.93 1.69 0.00
0.48 0.47 -1.55 2.69 1.39 0.00 0.54 -2.57 0.00 -0.35 0.00 4.55 4.55
2.09 0.00 -2.78 4.65 6.06 -4.35 3.67 1.29 -1.59 0.00 4.02 -2.46 -0.75 2.97 0.00
 1.87 3.18 1.45 2.15 1.80 0.00 -0.70 -5.12 0.00 -4.17 0.00 4.55 4.55
1.16 0.00 0.53 0.23 0.23 -0.12 0.96 0.90 4.01 0.00 0.54 2.53 2.04 0.05 0.00 1.1
3 0.19 -0.10 -0.16 2.71 0.00 5.58 -3.99 0.00 -0.72 0.00 4.55 4.55
3.66 0.00 1.79 3.71 3.18 -3.66 8.67 -0.41 -1.92 0.00 -0.21 -3.31 -2.18 2.83 0.0
0 2.25 1.31 -1.17 5.03 2.47 0.00 0.75 -5.01 0.00 -3.54 0.00 4.55 4.55
4.50 0.00 0.40 3.83 3.40 -4.36 7.52 -0.15 -1.59 0.00 0.27 -2.44 -1.29 2.59 0.00
 2.36 3.12 -1.05 2.98 2.86 0.00 0.88 -6.11 0.00 -3.89 0.00 4.55 4.55
0.96 0.00 -1.81 4.77 4.96 -2.52 1.47 4.99 -0.03 0.00 0.98 -0.76 -0.97 2.73 0.00
 1.00 3.31 0.97 -0.03 0.63 0.00 0.49 -4.86 0.00 -0.93 0.00 4.55 4.55
6.08 0.00 0.63 2.84 2.19 -2.71 2.52 0.01 1.70 0.00 0.60 -0.14 0.46 1.20 0.00 1.
99 1.38 -0.68 1.74 2.05 0.00 1.91 -4.48 0.00 -2.05 0.00 4.55 4.55
0.64 0.00 -1.96 -1.22 -0.54 4.31 0.80 -1.52 4.27 0.00 -1.81 5.56 4.33 -1.14 0.0
0 -0.96 -0.78 -2.62 -0.34 0.60 0.00 4.56 -0.41 0.00 0.63 0.00 4.55 4.55


  [Part of this file has been deleted for brevity]

0.68 0.00 -0.46 3.83 2.79 -1.46 1.37 3.83 -1.48 0.00 1.16 -1.91 -2.02 6.82 0.00
 -0.89 1.86 -0.16 0.74 0.55 0.00 -1.76 -1.09 0.00 1.29 0.00 4.55 4.55
-1.76 0.00 -1.47 -5.11 -3.02 7.73 -3.04 -0.48 3.60 0.00 -3.02 7.19 3.72 -2.84 0
.00 -1.20 -3.38 -2.45 -1.41 -1.11 0.00 2.18 5.11 0.00 5.28 0.00 4.55 4.55
0.46 0.00 -3.38 2.90 3.62 -4.43 0.41 2.59 -1.76 0.00 5.62 -2.10 0.37 2.26 0.00
2.21 4.56 5.10 1.00 0.58 0.00 -1.45 -0.16 0.00 -4.33 0.00 4.55 4.55
-1.37 0.00 -1.85 -4.16 -2.80 8.65 -3.47 -0.72 4.79 0.00 -2.93 8.47 5.65 -2.59 0
.00 -3.01 -2.44 -3.24 -2.58 -1.09 0.00 4.21 4.61 0.00 4.92 0.00 4.55 4.55
-0.92 0.00 -2.85 -3.67 -2.36 7.63 -3.04 -1.53 6.73 0.00 -2.36 9.07 6.57 -2.83 0
.00 -2.18 -1.98 -2.83 -2.16 -0.37 0.00 5.88 2.31 0.00 2.95 0.00 4.55 4.55
2.50 0.00 1.34 2.36 2.18 -3.29 4.63 -0.88 -1.28 0.00 3.40 -2.89 -1.22 2.55 0.00
 2.15 0.77 1.35 6.78 2.17 0.00 -0.38 -0.55 0.00 -3.65 0.00 4.55 4.55
1.02 0.00 -1.72 3.71 4.55 -2.08 1.58 4.50 -0.15 0.00 1.28 -0.72 -0.80 4.39 0.00
 0.76 2.95 0.85 0.40 0.82 0.00 0.37 -4.04 0.00 -0.70 0.00 4.55 4.55
3.93 0.00 3.10 -1.45 -1.41 0.69 1.36 -1.22 3.44 0.00 -2.02 1.49 1.37 -1.29 0.00
 1.02 -1.35 -2.31 1.39 1.47 0.00 4.57 -4.96 0.00 1.71 0.00 4.55 4.55
1.56 0.00 -2.33 -1.98 -1.19 5.27 -1.79 -1.53 6.20 0.00 -1.58 7.38 5.92 -1.92 0.
00 -0.93 -0.74 -2.57 -1.25 0.54 0.00 5.64 -0.10 0.00 0.99 0.00 4.55 4.55
2.04 0.00 -1.15 -1.62 -1.07 3.84 -0.65 -1.64 6.31 0.00 -1.46 6.55 5.21 -1.80 0.
00 -0.27 -0.80 -2.45 -0.89 0.89 0.00 6.71 -1.83 0.00 0.39 0.00 4.55 4.55
1.22 0.00 2.14 -0.07 -0.16 -0.32 1.17 0.93 2.98 0.00 0.15 0.88 0.71 0.11 0.00 1
.22 -0.17 0.12 1.82 1.14 0.00 4.24 -3.30 0.00 0.14 0.00 4.55 4.55
1.74 0.00 1.45 -0.36 -0.36 0.61 1.35 -1.63 6.05 0.00 -0.36 3.35 2.72 -0.81 0.00
 0.88 -1.31 -1.63 0.37 5.00 0.00 6.82 -4.87 0.00 -1.01 0.00 4.55 4.55
1.42 0.00 -3.76 -2.40 -1.34 6.13 -2.08 -1.38 5.20 0.00 -1.73 8.38 6.78 -2.06 0.
00 -1.08 -0.46 -2.71 -1.68 0.11 0.00 5.21 1.32 0.00 1.27 0.00 4.55 4.55
6.12 0.00 0.01 3.88 3.23 -3.77 2.78 2.33 -0.81 0.00 1.45 -1.51 -0.83 2.52 0.00
2.43 2.67 0.03 1.66 1.81 0.00 -0.03 -4.64 0.00 -1.76 0.00 4.55 4.55
2.54 0.00 0.90 1.55 1.86 -1.97 2.03 1.15 0.76 0.00 1.32 -0.58 0.08 1.35 0.00 2.
06 0.94 1.21 2.83 2.93 0.00 1.42 -1.60 0.00 -1.96 0.00 4.55 4.55
-0.44 0.00 -0.44 1.18 1.18 -0.72 -0.83 6.01 0.50 0.00 1.15 0.18 0.26 1.53 0.00
1.40 2.54 3.53 -0.83 -0.15 0.00 1.27 -0.07 0.00 0.13 0.00 4.55 4.55
0.82 0.00 -1.50 -2.02 -0.88 4.57 -1.52 1.23 3.02 0.00 -1.69 5.41 3.38 -0.96 0.0
0 -0.72 -0.66 -1.61 -1.21 -0.25 0.00 2.80 1.54 0.00 2.95 0.00 4.55 4.55
5.17 0.00 1.23 2.19 1.95 -4.22 5.46 0.10 -1.43 0.00 0.11 -2.40 -1.43 1.23 0.00
6.69 1.81 -0.05 3.39 2.55 0.00 1.10 -6.29 0.00 -4.67 0.00 4.55 4.55
4.19 0.00 -0.43 3.35 2.96 -4.08 5.31 0.07 -1.53 0.00 2.90 -2.53 -0.81 3.90 0.00
 1.77 2.05 0.28 2.97 2.31 0.00 0.14 -4.14 0.00 -3.30 0.00 4.55 4.55
1.99 0.00 -3.87 9.25 7.73 -6.29 3.74 2.72 -1.45 0.00 2.91 -3.15 -2.17 4.05 0.00
 0.73 4.23 0.49 1.45 1.45 0.00 -1.45 -7.25 0.00 -3.69 0.00 4.55 4.55
-1.21 0.00 -0.88 -5.63 -3.49 8.10 -3.04 -0.73 2.90 0.00 -3.14 6.59 2.49 -2.60 0
.00 -3.05 -4.32 -2.26 -0.90 -1.45 0.00 0.84 6.29 0.00 7.23 0.00 4.55 4.55
3.45 0.00 1.70 2.54 2.27 -3.00 6.03 -1.06 -0.10 0.00 0.63 -2.00 -1.00 2.06 0.00
 2.24 0.09 -1.15 3.73 7.15 0.00 1.27 -4.89 0.00 -3.06 0.00 4.55 4.55
3.63 0.00 0.32 0.13 0.96 -1.48 1.56 0.76 -0.13 0.00 -0.20 0.06 -0.26 -0.06 0.00
 5.87 0.79 0.10 1.87 1.48 0.00 0.81 -3.39 0.00 -2.18 0.00 4.55 4.55
4.89 0.00 -1.70 5.71 6.41 -4.71 3.81 1.67 -1.03 0.00 1.37 -2.04 -1.31 2.70 0.00
 2.79 3.25 -0.37 2.05 1.96 0.00 -0.34 -7.09 0.00 -3.47 0.00 4.55 4.55
2.59 0.00 -0.99 -0.55 -0.24 0.95 0.55 -1.22 4.26 0.00 0.89 4.17 3.90 -0.71 0.00
 0.68 0.05 -0.90 -0.08 1.27 0.00 5.74 -2.63 0.00 -1.04 0.00 4.55 4.55
0.43 0.00 -3.37 2.50 2.70 -1.54 -0.18 5.16 -0.75 0.00 1.36 0.96 0.74 2.75 0.00
1.00 6.23 1.89 -1.08 -0.54 0.00 -0.42 -1.36 0.00 -0.97 0.00 4.55 4.55
6.97 0.00 1.05 1.63 1.75 -2.35 4.47 -1.19 0.29 0.00 0.24 0.21 1.34 1.15 0.00 2.
37 1.01 -1.28 2.95 2.32 0.00 1.79 -4.77 0.00 -2.41 0.00 4.55 4.55
6.11 0.00 3.48 1.74 1.74 -2.76 4.35 -1.16 -0.43 0.00 0.87 -2.03 -1.30 1.89 0.00
 3.19 0.15 -0.44 7.68 2.47 0.00 0.15 -1.03 0.00 -2.61 0.00 4.55 4.55
-1.24 0.00 -2.27 -3.72 -2.76 6.98 -3.57 -0.76 3.20 0.00 -1.11 7.29 6.27 -2.03 0
.00 -3.11 -1.60 -0.58 -2.20 -1.12 0.00 2.66 3.14 0.00 3.74 0.00 4.55 4.55
1.53 0.00 -2.18 4.97 3.77 -3.67 2.06 2.19 0.68 0.00 1.79 -0.83 -0.49 3.86 0.00
0.68 4.09 0.41 0.73 1.71 0.00 0.34 -4.67 0.00 -2.33 0.00 4.55 4.55
0.39 0.00 -1.13 0.83 0.70 -2.97 -0.46 0.22 0.11 0.00 7.11 -2.15 0.66 1.56 0.00
0.54 1.17 3.70 1.79 1.45 0.00 -0.13 -1.33 0.00 -1.84 0.00 4.55 4.55
2.37 0.00 1.02 -2.12 -1.28 3.29 -0.07 -1.35 5.20 0.00 -1.89 4.81 2.92 -1.58 0.0
0 -0.33 -2.03 -2.60 -0.13 0.80 0.00 4.96 -1.19 0.00 2.09 0.00 4.55 4.55
-0.31 0.00 -2.90 -3.09 -2.12 6.97 -2.43 -1.32 5.92 0.00 -2.18 8.89 6.83 -2.54 0
.00 -1.76 -1.21 -2.85 -2.36 -0.31 0.00 6.51 1.66 0.00 2.19 0.00 4.55 4.55
5.05 0.00 -0.67 2.76 3.42 -1.63 2.78 0.05 0.51 0.00 0.46 0.47 0.67 1.46 0.00 1.
65 1.52 -1.22 2.76 1.73 0.00 1.06 -3.42 0.00 -1.92 0.00 4.55 4.55
1.58 0.00 -0.27 1.40 1.82 -1.02 3.17 -0.17 -0.12 0.00 1.04 -0.31 0.68 1.22 0.00
 1.41 0.89 1.05 3.93 1.20 0.00 0.78 0.56 0.00 -2.58 0.00 4.55 4.55
0.53 0.00 0.93 -2.26 -1.56 3.27 0.40 -1.70 5.52 0.00 -1.56 5.25 3.41 -1.74 0.00
 -0.13 -2.12 -2.00 0.88 0.68 0.00 6.52 -0.72 0.00 1.13 0.00 4.55 4.55
5.99 0.00 1.95 1.54 1.54 -3.21 3.07 -0.08 -0.64 0.00 1.57 -1.79 -0.35 1.52 0.00
 3.13 1.10 1.24 4.80 1.98 0.00 0.10 -0.48 0.00 -2.82 0.00 4.55 4.55
0.82 0.00 0.45 1.16 0.98 -0.33 0.46 1.04 0.65 0.00 2.38 -0.48 -0.02 3.38 0.00 -
0.39 0.12 0.15 0.88 3.55 0.00 0.14 -0.54 0.00 0.34 0.00 4.55 4.55
3.67 0.00 0.37 2.14 1.42 -1.78 2.48 -0.43 2.72 0.00 -0.12 1.29 1.07 0.40 0.00 1
.32 0.67 -1.36 0.73 1.55 0.00 4.17 -5.19 0.00 -1.53 0.00 0.92 0.92
-0.39 0.00 -2.72 -2.37 -1.58 5.92 -2.57 -1.40 6.20 0.00 -1.58 7.51 5.92 -2.18 0
.00 -1.58 -1.00 -2.18 -1.77 0.02 0.00 5.38 0.94 0.00 1.38 0.00 0.92 0.92
5.69 0.00 1.02 1.58 1.58 -2.62 2.72 -0.47 0.30 0.00 1.34 -0.72 0.12 1.31 0.00 2
.31 0.68 -0.69 2.05 4.59 0.00 0.95 -3.79 0.00 -1.97 0.00 0.92 0.92
2.81 0.00 1.15 1.76 1.76 -1.90 1.70 2.20 -0.87 0.00 1.52 -1.53 -1.05 2.07 0.00
1.98 1.40 1.17 3.51 1.15 0.00 -0.59 -0.63 0.00 -1.10 0.00 0.92 0.92
0.18 0.00 -3.57 2.22 2.52 -3.57 -0.23 0.78 -1.19 0.00 8.20 -1.79 0.95 2.44 0.00
 0.60 2.51 4.27 1.19 1.19 0.00 -1.19 -0.14 0.00 -3.51 0.00 0.92 0.92
-1.60 0.00 4.97 -2.92 -2.79 7.25 -3.39 1.42 0.90 0.00 -3.08 2.34 0.39 -0.72 0.0
0 -4.40 -3.21 -3.08 -2.32 -1.60 0.00 -0.17 5.69 0.00 7.95 0.00 0.92 0.92
-0.69 0.00 -1.86 1.52 1.46 -2.40 -0.89 4.21 -1.64 0.00 4.26 -1.88 -0.02 2.60 0.
00 1.14 2.74 5.28 0.32 0.02 0.00 -1.64 2.53 0.00 -1.65 0.00 0.92 0.92
0.61 0.00 -1.16 2.35 2.76 -1.47 1.08 0.82 -0.41 0.00 0.61 -0.74 -0.53 1.08 0.00
 0.20 1.23 0.00 0.41 0.41 0.00 -0.41 -2.25 0.00 -1.02 0.00 0.92 0.92
0.78 0.00 -0.96 -0.53 -0.24 1.41 -0.35 -0.35 1.14 0.00 -0.43 2.08 1.71 -0.45 0.
00 -0.12 -0.02 -0.76 -0.33 0.10 0.00 1.27 0.22 0.00 0.24 0.00 0.92 0.92
1.78 0.00 0.47 1.04 0.90 -1.16 2.51 -0.35 -0.43 0.00 -0.14 -0.78 -0.43 0.69 0.0
0 0.74 0.41 -0.61 1.10 0.82 0.00 0.41 -1.92 0.00 -1.04 0.00 0.92 0.92
-0.43 0.00 1.43 -0.71 -0.71 1.86 -0.86 0.43 0.14 0.00 -0.86 0.43 -0.14 -0.14 0.
00 -1.14 -0.86 -0.86 -0.57 -0.43 0.00 -0.14 1.57 0.00 2.14 0.00 0.92 0.92
0.29 0.00 -0.86 0.86 0.86 -1.14 0.29 0.86 -0.43 0.00 0.57 -0.14 0.00 0.57 0.00
0.43 2.14 0.57 -0.14 -0.14 0.00 -0.29 -0.71 0.00 -0.86 0.00 0.92 0.92
0.86 0.00 0.29 0.86 0.71 -0.86 2.14 -0.29 -0.43 0.00 -0.14 -0.71 -0.43 0.57 0.0
0 0.43 0.29 -0.43 0.86 0.57 0.00 0.29 -1.43 0.00 -0.86 0.00 0.92 0.92

  Simple frequency matrix

   The columns represent amino acid counts for the amino acid residues
   from A to Z. The rows represent the alignment positions from 1->n. The
   file is a "Simple" frequency matrix of "Length" 20 amino acids. The
   maximum score this matrix can give is 496. The "Threshold" value is an
   instruction to the profit application to only report matches above the
   given score.

  Gribskov profile

   The columns represent the amino acids from A to Z, the rows denote the
   alignment position from 1 to n. The last column is the indel penalty.
   The "Name" is the name used by prophet to refer to the profile, the
   "Matrix" is the name of the scoring matrix used (containing residue
   substitution values). "Length" is the length of the alignment.
   "Max_score" is the maximum score this profile can produce. The
   threshold is an instruction to prophet to only report hits equal to or
   above the given value. The gap opening and extension values are used
   by prophet in the dynamic alignment (Smith Waterman equivalent).

Data files

   The two profile methods require a residue substitution scoring matrix.

   The Gribskov marices use the data file 'Epprofile' by default. This is
   derived from a PAM250 scoring matrix.

   The Henikoff matrices use the data file 'EBLOSUM62' by default.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   None.

References

    1. Gribskov M, McLachlan AD, Eisenberg D. Proc Natl Acad Sci U S A.
       1987 Jul; 84(13): 4355-8.
    2. Henikoff S, Henikoff JG. J Mol Biol. 1994 Nov 4; 243(4): 574-8.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                     Description
   profit       Scan a sequence or database with a matrix or profile
   prophet      Gapped alignment for profiles

Author(s)

   Alan Bleasby (ajb