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OPENSEQ.org
cI_A_20_cytb_20_human
Genes: A B A+B
Length: 115 378 489
Sequences: 5998 4474 3440
Seq/Len: 52.16 11.84 7.03
MirrorTree (Pazo et al. 2001) 0.75
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 0.09
2 0.00 0.00 0.29
5 0.00 0.00 5.11
10 0.00 0.00 5.71
20 0.00 0.00 5.78
100 0.00 0.00 5.93
∞ 0.01 0.00 6.98
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
71_L 301_L 1.16 0.95 0.21
94_L 257_T 0.96 0.83 0.11
87_M 322_Q 0.94 0.82 0.11
31_M 169_S 0.88 0.76 0.09
67_L 318_R 0.88 0.75 0.09
100_L 377_L 0.87 0.75 0.08
52_S 252_D 0.85 0.72 0.08
94_L 123_T 0.84 0.71 0.07
70_A 129_M 0.84 0.70 0.07
99_A 26_N 0.83 0.70 0.07
54_K 105_G 0.82 0.68 0.07
87_M 160_L 0.82 0.68 0.07
20_I 350_I 0.81 0.67 0.07
64_L 361_T 0.79 0.64 0.06
72_L 162_Q 0.78 0.62 0.06
44_M 47_T 0.78 0.61 0.06
92_L 368_T 0.75 0.58 0.05
60_I 58_D 0.74 0.57 0.05
56_F 25_S 0.74 0.56 0.05
71_L 67_A 0.74 0.56 0.05
37_Y 237_L 0.74 0.56 0.05
29_G 243_T 0.73 0.55 0.05
72_L 75_Y 0.73 0.54 0.05
11_T 292_L 0.73 0.54 0.05
58_V 348_T 0.72 0.53 0.05
17_L 56_S 0.72 0.53 0.05
54_K 108_L 0.71 0.52 0.05
76_P 58_D 0.71 0.52 0.04
12_L 46_T 0.71 0.52 0.04
100_L 300_I 0.71 0.52 0.04
60_I 57_P 0.71 0.52 0.04
16_L 190_A 0.71 0.51 0.04
60_I 96_L 0.71 0.51 0.04
27_L 27_I 0.71 0.51 0.04
61_T 62_A 0.71 0.51 0.04
108_Q 29_A 0.69 0.49 0.04
79_X 153_I 0.69 0.49 0.04
73_L 222_P 0.69 0.49 0.04
81_T 47_T 0.69 0.49 0.04
46_P 225_T 0.69 0.49 0.04
31_M 67_A 0.69 0.48 0.04
6_I 27_I 0.69 0.48 0.04
102_L 244_L 0.68 0.47 0.04
106_W 337_W 0.68 0.46 0.04
103_A 243_T 0.67 0.45 0.04
59_A 62_A 0.67 0.45 0.04
76_P 176_T 0.67 0.45 0.04
91_S 160_L 0.66 0.44 0.04
108_Q 322_Q 0.66 0.44 0.04
13_L 43_L 0.66 0.43 0.04
20_I 118_I 0.65 0.43 0.04
5_L 364_I 0.65 0.43 0.04
86_L 111_E 0.65 0.42 0.04
103_A 350_I 0.65 0.42 0.03
7_L 243_T 0.64 0.41 0.03
51_F 339_G 0.64 0.40 0.03
104_Y 64_S 0.64 0.40 0.03
36_P 222_P 0.63 0.39 0.03
14_A 158_T 0.63 0.39 0.03
13_L 148_N 0.63 0.39 0.03
19_I 303_M 0.63 0.39 0.03
32_E 251_G 0.63 0.39 0.03
85_P 292_L 0.62 0.38 0.03
103_A 81_Y 0.62 0.38 0.03
81_T 195_L 0.62 0.37 0.03
20_I 357_L 0.62 0.37 0.03
101_S 107_F 0.62 0.37 0.03
45_S 308_H 0.61 0.37 0.03
42_D 101_G 0.61 0.36 0.03
63_L 85_N 0.61 0.36 0.03
56_F 153_I 0.61 0.36 0.03
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)
ID Seq/Len Name Options I_Prob Status
5614 1.96 cI_A_40_cytb_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2016_06b) 0.88 Done - Shared
5613 1.95 cI_A_40_cytb_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.92 Done - Shared
5612 7.03 cI_A_20_cytb_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.21 Done - Shared
5611 1.93 cI_A_40_cytb_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.89 Done - Shared
5610 1.94 cI_A_40_cytb_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) 0.85 Done - Shared
5596 0 cI_A_60_cytb_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5593 0 cI_A_80_cytb_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5591 1.95 cI_A_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.85 Done - Shared
5586 7.85 cI_A_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.03 Done - Shared
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