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OPENSEQ.org
test1
Genes: A B A+B
Length: 201 241 413
Sequences: 3022 3244 72
Seq/Len: 15.03 13.46 0.17
MirrorTree (Pazo et al. 2001) 0.32
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.12 0.13 0.06
2 0.12 0.14 0.08
5 0.13 0.15 0.11
10 0.13 0.16 0.15
20 0.14 0.17 0.16
100 0.16 0.19 0.21
∞ 0.18 0.21 0.30
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
33_W 32_W 1.82 0.46 0.00
138_D 214_L 1.61 0.34 0.00
170_S 193_V 1.39 0.24 0.00
161_L 120_P 1.36 0.23 0.00
34_Y 222_Q 1.35 0.22 0.00
33_W 156_W 1.29 0.20 0.00
79_R 122_V 1.28 0.20 0.00
107_L 156_W 1.28 0.20 0.00
101_F 139_T 1.25 0.18 0.00
126_S 142_C 1.24 0.18 0.00
136_F 209_V 1.23 0.18 0.00
87_I 210_Q 1.22 0.17 0.00
20_C 21_C 1.20 0.17 0.00
174_V 154_L 1.18 0.16 0.00
37_L 120_P 1.17 0.16 0.00
161_L 135_T 1.17 0.16 0.00
80_D 224_R 1.16 0.15 0.00
141_S 23_P 1.14 0.15 0.00
33_W 191_L 1.12 0.14 0.00
84_Y 231_I 1.11 0.14 0.00
145_V 11_A 1.11 0.14 0.00
16_V 108_L 1.09 0.14 0.00
80_D 156_W 1.08 0.13 0.00
138_D 203_N 1.08 0.13 0.00
14_E 229_T 1.05 0.12 0.00
93_G 211_F 1.05 0.12 0.00
138_D 80_T 1.04 0.12 0.00
34_Y 168_S 1.04 0.12 0.00
130_D 17_V 1.03 0.12 0.00
33_W 88_Y 1.03 0.12 0.00
31_I 205_F 1.01 0.12 0.00
57_M 222_Q 1.01 0.12 0.00
170_S 149_P 1.00 0.11 0.00
84_Y 32_W 0.99 0.11 0.00
80_D 222_Q 0.98 0.11 0.00
33_W 149_P 0.98 0.11 0.00
119_A 149_P 0.97 0.11 0.00
67_K 193_V 0.97 0.11 0.00
70_T 194_S 0.97 0.10 0.00
106_I 216_E 0.97 0.10 0.00
122_Q 234_A 0.96 0.10 0.00
86_C 149_P 0.96 0.10 0.00
109_V 209_V 0.96 0.10 0.00
33_W 214_L 0.96 0.10 0.00
80_D 32_W 0.95 0.10 0.00
66_R 27_H 0.95 0.10 0.00
142_Q 114_L 0.95 0.10 0.00
120_V 146_G 0.94 0.10 0.00
183_A 92_S 0.94 0.10 0.00
13_E 234_A 0.94 0.10 0.00
172_S 209_V 0.94 0.10 0.00
107_L 214_L 0.94 0.10 0.00
128_S 144_A 0.94 0.10 0.00
90_L 160_G 0.94 0.10 0.00
101_F 103_G 0.94 0.10 0.00
82_A 154_L 0.93 0.10 0.00
124_R 78_Q 0.93 0.10 0.00
126_S 77_I 0.92 0.10 0.00
176_W 49_N 0.92 0.10 0.00
45_V 80_T 0.92 0.10 0.00
79_R 93_S 0.91 0.09 0.00
93_G 153_E 0.91 0.09 0.00
178_N 171_P 0.91 0.09 0.00
175_A 132_I 0.90 0.09 0.00
129_S 139_T 0.90 0.09 0.00
177_S 79_R 0.90 0.09 0.00
86_C 110_V 0.90 0.09 0.00
163_M 17_V 0.89 0.09 0.00
82_A 65_A 0.89 0.09 0.00
88_L 193_V 0.89 0.09 0.00
153_V 171_P 0.89 0.09 0.00
161_L 193_V 0.89 0.09 0.00
161_L 13_R 0.88 0.09 0.00
96_Y 64_F 0.88 0.09 0.00
34_Y 144_A 0.88 0.09 0.00
96_Y 62_R 0.88 0.09 0.00
96_Y 135_T 0.87 0.09 0.00
64_E 84_D 0.87 0.09 0.00
118_P 104_P 0.87 0.09 0.00
161_L 96_Q 0.87 0.09 0.00
21_N 119_P 0.87 0.09 0.00
176_W 44_L 0.87 0.09 0.00
95_S 88_Y 0.87 0.09 0.00
141_S 209_V 0.87 0.09 0.00
167_D 174_L 0.87 0.09 0.00
121_Y 163_V 0.86 0.09 0.00
73_L 192_R 0.86 0.09 0.00
82_A 219_E 0.86 0.09 0.00
130_D 214_L 0.86 0.08 0.00
115_N 70_G 0.86 0.08 0.00
18_L 220_W 0.86 0.08 0.00
176_W 77_I 0.86 0.08 0.00
60_L 169_T 0.85 0.08 0.00
79_R 207_C 0.85 0.08 0.00
4_Q 88_Y 0.85 0.08 0.00
124_R 224_R 0.85 0.08 0.00
148_S 120_P 0.85 0.08 0.00
170_S 139_T 0.85 0.08 0.00
153_V 78_Q 0.85 0.08 0.00
114_Q 161_K 0.84 0.08 0.00
176_W 21_C 0.84 0.08 0.00
82_A 11_A 0.84 0.08 0.00
86_C 21_C 0.84 0.08 0.00
93_G 160_G 0.84 0.08 0.00
96_Y 232_V 0.83 0.08 0.00
119_A 192_R 0.83 0.08 0.00
95_S 136_Q 0.83 0.08 0.00
56_R 23_P 0.83 0.08 0.00
141_S 49_N 0.83 0.08 0.00
176_W 75_L 0.83 0.08 0.00
187_A 228_V 0.83 0.08 0.00
82_A 88_Y 0.82 0.08 0.00
56_R 225_A 0.82 0.08 0.00
141_S 218_D 0.82 0.08 0.00
129_S 109_T 0.82 0.08 0.00
121_Y 30_L 0.82 0.08 0.00
84_Y 74_T 0.82 0.08 0.00
70_T 143_L 0.82 0.08 0.00
14_E 138_A 0.82 0.08 0.00
123_L 122_V 0.81 0.08 0.00
71_L 77_I 0.81 0.08 0.00
109_V 91_A 0.81 0.08 0.00
175_A 226_K 0.81 0.08 0.00
148_S 140_L 0.81 0.08 0.00
18_L 153_E 0.81 0.08 0.00
120_V 174_L 0.81 0.08 0.00
106_I 160_G 0.81 0.07 0.00
60_L 30_L 0.81 0.07 0.00
101_F 51_A 0.81 0.07 0.00
103_Q 216_E 0.81 0.07 0.00
82_A 32_W 0.81 0.07 0.00
151_S 142_C 0.81 0.07 0.00
122_Q 136_Q 0.80 0.07 0.00
180_S 120_P 0.80 0.07 0.00
102_G 17_V 0.80 0.07 0.00
37_L 209_V 0.80 0.07 0.00
121_Y 122_V 0.80 0.07 0.00
59_S 13_R 0.80 0.07 0.00
142_Q 120_P 0.80 0.07 0.00
134_C 157_W 0.80 0.07 0.00
45_V 190_R 0.80 0.07 0.00
43_E 209_V 0.80 0.07 0.00
149_K 120_P 0.80 0.07 0.00
123_L 30_L 0.80 0.07 0.00
75_R 77_I 0.80 0.07 0.00
164_R 199_Q 0.79 0.07 0.00
128_S 62_R 0.79 0.07 0.00
148_S 99_E 0.79 0.07 0.00
126_S 207_C 0.79 0.07 0.00
145_V 199_Q 0.79 0.07 0.00
13_E 150_D 0.79 0.07 0.00
27_G 209_V 0.79 0.07 0.00
132_S 230_Q 0.78 0.07 0.00
96_Y 207_C 0.78 0.07 0.00
19_P 87_V 0.78 0.07 0.00
28_T 115_K 0.78 0.07 0.00
122_Q 219_E 0.78 0.07 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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