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OPENSEQ.org
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Genes: A B A+B
Length: 67 122 184
Sequences: 6161 89235 3711
Seq/Len: 91.96 731.43 20.17
MirrorTree (Pazo et al. 2001) 0.52
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 0.11 19.63
2 0.00 0.13 20.37
5 0.01 0.16 21.28
10 0.02 0.19 22.75
20 0.04 0.23 24.42
100 0.10 0.31 29.25
∞ 0.16 0.34 31.14
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
41_E 16_K 2.72 1.00 1.00
22_A 17_I 2.66 1.00 1.00
25_E 108_S 2.46 1.00 1.00
18_T 14_L 2.09 1.00 0.99
26_T 21_N 2.05 1.00 0.99
49_Q 13_V 1.70 1.00 0.97
48_D 13_V 1.64 1.00 0.96
42_F 20_F 1.60 1.00 0.95
23_Y 17_I 1.49 1.00 0.93
29_N 21_N 1.09 0.96 0.70
15_T 11_S 1.04 0.94 0.65
30_S 24_K 1.03 0.94 0.63
38_T 23_K 0.98 0.91 0.58
23_Y 16_K 0.96 0.90 0.56
45_V 13_V 0.96 0.90 0.56
29_N 110_S 0.95 0.90 0.54
19_A 14_L 0.95 0.89 0.54
14_R 104_R 0.94 0.89 0.53
7_A 85_K 0.86 0.82 0.42
18_T 107_F 0.83 0.79 0.39
25_E 88_E 0.76 0.70 0.30
38_T 20_F 0.75 0.68 0.29
26_T 20_F 0.72 0.64 0.26
29_N 109_P 0.68 0.57 0.21
29_N 24_K 0.67 0.55 0.20
45_V 17_I 0.65 0.52 0.19
6_I 9_D 0.61 0.46 0.16
12_E 83_T 0.60 0.44 0.15
3_T 87_G 0.58 0.40 0.13
26_T 109_P 0.57 0.39 0.12
15_T 55_M 0.57 0.38 0.12
14_R 86_G 0.56 0.38 0.12
25_E 109_P 0.55 0.35 0.11
3_T 89_E 0.55 0.35 0.11
15_T 88_E 0.51 0.29 0.09
40_K 28_E 0.49 0.27 0.08
65_R 86_G 0.48 0.26 0.07
55_N 50_I 0.48 0.26 0.07
34_L 24_K 0.46 0.23 0.06
58_N 86_G 0.45 0.22 0.06
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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