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OPENSEQ.org
cIV_B_40_cI_H_40_human
Genes: A B A+B
Length: 227 318 540
Sequences: 4037 4127 2708
Seq/Len: 17.78 12.98 5.01
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 0.15
2 0.00 0.00 0.33
5 0.00 0.00 2.07
10 0.00 0.00 3.79
20 0.00 0.01 3.94
100 0.01 0.01 4.05
∞ 0.01 0.02 4.97
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
12_A 116_I 0.98 0.77 0.02
205_S 209_S 0.92 0.70 0.01
33_L 118_W 0.87 0.64 0.01
202_A 176_L 0.86 0.63 0.01
74_V 271_L 0.86 0.63 0.01
127_F 87_T 0.86 0.63 0.01
155_T 128_A 0.84 0.60 0.01
29_M 165_L 0.84 0.60 0.01
90_V 132_A 0.83 0.59 0.01
116_L 132_A 0.83 0.59 0.01
61_M 144_V 0.83 0.59 0.01
25_D 205_S 0.82 0.58 0.01
152_M 179_W 0.82 0.58 0.01
34_I 46_L 0.82 0.57 0.01
175_I 118_W 0.82 0.57 0.01
160_L 132_A 0.81 0.57 0.01
192_Y 78_A 0.81 0.56 0.01
99_S 79_L 0.80 0.55 0.01
184_F 115_S 0.80 0.55 0.01
168_L 147_A 0.80 0.54 0.01
144_L 237_L 0.79 0.54 0.01
87_T 52_A 0.78 0.52 0.01
189_P 144_V 0.77 0.50 0.01
38_V 193_T 0.77 0.50 0.01
16_I 271_L 0.77 0.50 0.01
213_L 74_A 0.76 0.49 0.01
24_H 114_Y 0.76 0.49 0.01
162_S 217_A 0.76 0.49 0.01
195_Q 224_F 0.75 0.48 0.01
203_N 212_N 0.75 0.48 0.01
97_I 260_V 0.75 0.48 0.01
2_A 97_N 0.75 0.47 0.01
168_L 89_L 0.74 0.46 0.01
37_L 270_F 0.74 0.46 0.01
9_L 135_A 0.73 0.46 0.01
28_L 132_A 0.73 0.45 0.01
188_R 188_S 0.73 0.44 0.01
110_Y 162_L 0.72 0.43 0.01
160_L 109_S 0.72 0.43 0.01
195_Q 21_M 0.71 0.43 0.01
23_F 209_S 0.71 0.43 0.01
104_W 224_F 0.71 0.42 0.01
223_P 6_L 0.71 0.42 0.01
32_F 13_I 0.71 0.42 0.01
133_L 146_L 0.71 0.42 0.01
148_T 307_M 0.71 0.42 0.01
70_A 189_T 0.71 0.41 0.01
150_I 9_L 0.71 0.41 0.01
127_F 309_I 0.71 0.41 0.01
92_D 259_F 0.70 0.41 0.01
99_S 95_L 0.70 0.41 0.01
19_E 277_Y 0.70 0.41 0.01
64_V 15_I 0.70 0.41 0.01
2_A 29_G 0.70 0.40 0.01
46_L 69_T 0.69 0.40 0.01
116_L 172_F 0.69 0.40 0.01
191_V 301_L 0.69 0.40 0.01
192_Y 119_S 0.69 0.40 0.01
55_I 154_L 0.69 0.39 0.01
76_I 26_K 0.69 0.39 0.01
215_P 16_A 0.69 0.39 0.01
7_V 159_S 0.69 0.39 0.01
28_L 163_S 0.69 0.39 0.01
90_V 280_F 0.69 0.39 0.01
95_L 11_V 0.69 0.39 0.01
215_P 308_P 0.68 0.39 0.01
206_F 144_V 0.68 0.38 0.01
178_R 121_W 0.68 0.38 0.01
37_L 232_I 0.68 0.38 0.01
164_A 108_T 0.68 0.38 0.01
97_I 184_M 0.68 0.38 0.01
60_E 155_L 0.68 0.38 0.01
8_G 244_G 0.68 0.37 0.01
143_V 257_T 0.67 0.37 0.01
80_S 21_M 0.67 0.37 0.01
72_I 3_M 0.67 0.37 0.01
147_E 82_A 0.67 0.37 0.01
175_I 302_M 0.67 0.37 0.01
144_L 108_T 0.67 0.36 0.01
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
4579 4.19 cIV_B_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4574 4.21 cIV_B_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4573 3.59 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4568 3.98 cIV_B_60_cI_H_80_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4567 3.6 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4565 4.2 cIV_B_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4564 5.01 cIV_B_40_cI_H_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4563 3.53 cIV_B_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
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