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OPENSEQ.org
Vik
Genes: A B A+B
Length: 173 362 528
Sequences: 3718 3426 1449
Seq/Len: 21.49 9.46 2.74
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.00 2.23
2 0.00 0.00 2.33
5 0.00 0.00 2.66
10 0.01 0.00 2.68
20 0.01 0.00 2.71
100 0.02 0.01 2.86
∞ 0.05 0.02 3.72
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
91_R 143_T 0.97 0.58 0.00
18_S 295_T 0.80 0.39 0.00
9_L 193_D 0.79 0.37 0.00
80_T 134_Q 0.77 0.35 0.00
12_P 81_L 0.75 0.33 0.00
163_A 179_A 0.75 0.33 0.00
155_D 326_L 0.71 0.28 0.00
102_Y 253_I 0.70 0.28 0.00
18_S 50_L 0.70 0.27 0.00
113_R 146_N 0.67 0.25 0.00
94_L 145_V 0.67 0.24 0.00
123_L 185_V 0.66 0.24 0.00
118_K 182_L 0.66 0.24 0.00
110_Q 262_W 0.66 0.24 0.00
26_Q 68_I 0.66 0.24 0.00
48_G 258_G 0.66 0.23 0.00
47_V 176_R 0.66 0.23 0.00
80_T 188_Y 0.65 0.23 0.00
101_V 14_P 0.65 0.23 0.00
168_H 144_A 0.65 0.23 0.00
77_V 29_L 0.64 0.22 0.00
75_G 40_V 0.64 0.22 0.00
77_V 131_L 0.64 0.22 0.00
15_A 82_D 0.64 0.22 0.00
153_R 327_A 0.63 0.21 0.00
79_A 337_A 0.63 0.21 0.00
7_I 185_V 0.62 0.21 0.00
130_R 338_I 0.62 0.20 0.00
133_L 263_L 0.62 0.20 0.00
47_V 266_E 0.61 0.20 0.00
7_I 46_A 0.61 0.20 0.00
88_R 337_A 0.61 0.20 0.00
137_A 38_M 0.60 0.19 0.00
13_M 334_L 0.60 0.19 0.00
97_R 88_L 0.60 0.19 0.00
114_T 26_A 0.60 0.19 0.00
77_V 134_Q 0.59 0.18 0.00
12_P 161_A 0.59 0.18 0.00
52_D 245_L 0.59 0.18 0.00
133_L 119_Q 0.59 0.18 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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