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OPENSEQ.org
1b-N brute (A, 30-100) (B, 70-780)
Genes: A B A+B
Length: 71 711 774
Sequences: 217 1479 86
Seq/Len: 3.06 2.08 0.11
MirrorTree (Pazo et al. 2001) 0.51
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.01 0.01
∞ 0.00 0.04 0.11
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
10_I 513_M 1.72 0.30 0.00
48_P 418_M 1.52 0.22 0.00
23_Y 104_L 1.41 0.19 0.00
12_A 490_E 1.39 0.18 0.00
10_I 584_Q 1.38 0.18 0.00
14_V 191_R 1.29 0.15 0.00
10_I 641_F 1.26 0.14 0.00
10_I 250_S 1.24 0.14 0.00
33_S 215_Y 1.22 0.13 0.00
61_E 369_I 1.21 0.13 0.00
24_F 104_L 1.19 0.13 0.00
15_L 482_Q 1.16 0.12 0.00
64_Q 298_K 1.14 0.12 0.00
29_K 345_F 1.12 0.11 0.00
16_V 591_R 1.11 0.11 0.00
14_V 663_K 1.11 0.11 0.00
63_R 99_Q 1.10 0.11 0.00
17_T 594_P 1.10 0.11 0.00
27_H 228_M 1.09 0.11 0.00
37_Q 412_S 1.09 0.11 0.00
56_Y 617_L 1.07 0.10 0.00
50_P 292_N 1.07 0.10 0.00
64_Q 642_A 1.07 0.10 0.00
57_I 633_T 1.07 0.10 0.00
21_G 402_E 1.06 0.10 0.00
14_V 85_M 1.06 0.10 0.00
15_L 383_K 1.04 0.10 0.00
65_P 373_F 1.03 0.10 0.00
63_R 305_N 1.03 0.10 0.00
52_E 637_V 1.02 0.09 0.00
23_Y 276_D 1.02 0.09 0.00
11_A 83_I 1.02 0.09 0.00
9_A 562_G 1.01 0.09 0.00
40_K 450_T 1.01 0.09 0.00
52_E 248_G 1.00 0.09 0.00
21_G 284_M 1.00 0.09 0.00
52_E 18_L 0.99 0.09 0.00
22_L 664_L 0.99 0.09 0.00
56_Y 161_L 0.98 0.09 0.00
53_R 341_P 0.98 0.09 0.00
59_E 380_A 0.98 0.09 0.00
65_P 652_T 0.97 0.09 0.00
10_I 467_A 0.97 0.09 0.00
50_P 510_N 0.96 0.08 0.00
64_Q 671_M 0.96 0.08 0.00
65_P 465_A 0.95 0.08 0.00
61_E 607_Q 0.95 0.08 0.00
65_P 568_L 0.95 0.08 0.00
46_L 76_F 0.94 0.08 0.00
21_G 674_Y 0.94 0.08 0.00
22_L 248_G 0.94 0.08 0.00
15_L 389_I 0.94 0.08 0.00
45_G 213_R 0.94 0.08 0.00
61_E 294_W 0.94 0.08 0.00
37_Q 595_A 0.93 0.08 0.00
53_R 264_Y 0.93 0.08 0.00
23_Y 111_L 0.93 0.08 0.00
54_W 145_L 0.93 0.08 0.00
10_I 285_V 0.93 0.08 0.00
55_R 609_V 0.93 0.08 0.00
57_I 517_L 0.92 0.08 0.00
42_T 421_G 0.92 0.08 0.00
15_L 471_L 0.91 0.08 0.00
58_K 349_V 0.91 0.08 0.00
32_E 562_G 0.91 0.07 0.00
58_K 170_E 0.91 0.07 0.00
35_T 109_D 0.91 0.07 0.00
59_E 541_L 0.91 0.07 0.00
4_S 348_L 0.91 0.07 0.00
19_I 681_Q 0.91 0.07 0.00
53_R 30_V 0.91 0.07 0.00
10_I 426_F 0.91 0.07 0.00
14_V 216_W 0.90 0.07 0.00
10_I 604_T 0.90 0.07 0.00
10_I 214_S 0.90 0.07 0.00
22_L 163_T 0.89 0.07 0.00
47_P 14_Y 0.89 0.07 0.00
47_P 492_G 0.89 0.07 0.00
8_V 700_D 0.89 0.07 0.00
8_V 223_Y 0.89 0.07 0.00
13_A 673_I 0.89 0.07 0.00
52_E 420_G 0.89 0.07 0.00
63_R 275_L 0.89 0.07 0.00
10_I 454_Q 0.88 0.07 0.00
61_E 551_E 0.88 0.07 0.00
10_I 117_M 0.88 0.07 0.00
15_L 439_I 0.88 0.07 0.00
24_F 368_K 0.88 0.07 0.00
42_T 601_T 0.88 0.07 0.00
19_I 40_R 0.88 0.07 0.00
48_P 170_E 0.88 0.07 0.00
67_V 176_L 0.87 0.07 0.00
13_A 149_R 0.87 0.07 0.00
51_E 163_T 0.87 0.07 0.00
43_G 500_L 0.87 0.07 0.00
62_S 386_V 0.87 0.07 0.00
13_A 269_P 0.87 0.07 0.00
21_G 285_V 0.87 0.07 0.00
13_A 187_L 0.87 0.07 0.00
65_P 484_D 0.87 0.07 0.00
18_F 667_A 0.87 0.07 0.00
51_E 594_P 0.87 0.07 0.00
9_A 450_T 0.87 0.07 0.00
19_I 349_V 0.87 0.07 0.00
25_I 345_F 0.86 0.07 0.00
44_N 605_M 0.86 0.07 0.00
13_A 219_A 0.86 0.07 0.00
15_L 582_L 0.86 0.07 0.00
18_F 261_A 0.86 0.07 0.00
65_P 694_I 0.86 0.07 0.00
65_P 377_A 0.86 0.07 0.00
58_K 22_I 0.86 0.07 0.00
67_V 673_I 0.85 0.07 0.00
9_A 693_D 0.85 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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