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OPENSEQ.org
cIV_A_10_cI_A_20_human
Genes: A B A+B
Length: 513 115 623
Sequences: 4400 4326 1903
Seq/Len: 8.58 37.62 3.05
MirrorTree (Pazo et al. 2001) 0.32
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 0.01 0.00 0.05
2 0.01 0.00 0.14
5 0.02 0.00 1.34
10 0.02 0.00 1.56
20 0.03 0.00 1.71
100 0.04 0.01 1.95
∞ 0.08 0.02 3.03
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
504_T 76_P 1.27 0.88 0.23
27_G 76_P 1.25 0.87 0.22
359_A 30_Y 1.03 0.68 0.11
17_T 56_F 1.03 0.68 0.11
215_L 108_Q 0.97 0.61 0.09
270_Y 75_L 0.91 0.54 0.07
5_R 76_P 0.91 0.54 0.07
7_L 18_M 0.90 0.54 0.07
328_H 36_P 0.90 0.53 0.07
181_T 15_L 0.89 0.52 0.07
412_I 69_I 0.89 0.52 0.07
410_A 26_Q 0.89 0.52 0.07
363_L 70_A 0.88 0.51 0.07
363_L 110_G 0.88 0.50 0.07
87_I 72_L 0.87 0.49 0.06
504_T 59_A 0.87 0.49 0.06
353_L 35_T 0.86 0.48 0.06
85_L 72_L 0.86 0.48 0.06
117_M 64_L 0.86 0.48 0.06
472_I 8_M 0.85 0.47 0.06
504_T 37_Y 0.85 0.47 0.06
42_G 59_A 0.85 0.47 0.06
220_F 113_W 0.85 0.47 0.06
333_K 16_L 0.85 0.46 0.06
29_L 70_A 0.84 0.46 0.06
155_V 25_P 0.84 0.46 0.06
274_V 37_Y 0.84 0.45 0.06
261_Y 87_M 0.83 0.44 0.05
314_I 12_L 0.81 0.41 0.05
12_H 113_W 0.80 0.41 0.05
289_A 113_W 0.80 0.41 0.05
274_V 67_L 0.80 0.40 0.05
374_V 93_L 0.79 0.40 0.05
24_A 11_T 0.79 0.39 0.05
350_V 7_L 0.79 0.39 0.05
447_Y 8_M 0.79 0.39 0.05
220_F 69_I 0.78 0.39 0.05
53_I 102_L 0.78 0.38 0.04
260_Y 56_F 0.77 0.38 0.04
505_F 58_V 0.77 0.38 0.04
473_W 9_I 0.77 0.37 0.04
340_W 52_S 0.76 0.36 0.04
159_L 106_W 0.76 0.36 0.04
504_T 104_Y 0.74 0.34 0.04
374_V 19_I 0.74 0.34 0.04
318_V 63_L 0.74 0.34 0.04
492_L 84_L 0.73 0.33 0.04
254_I 8_M 0.73 0.33 0.04
413_H 54_K 0.73 0.33 0.04
174_P 67_L 0.73 0.33 0.04
328_H 75_L 0.73 0.32 0.04
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
4474 0.34 cIV_A_20_cI_A_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4471 3.35 cIV_A_20_cI_A_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
4470 3.05 cIV_A_10_cI_A_20_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
4468 2.76 cIV_A_40_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4466 0.34 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4460 3.04 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.27 Done - Shared
4458 3.54 cIV_A_4_cI_A_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4456 0 cIV_A_80_cI_A_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) Killed - Shared
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