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OPENSEQ.org
take1
Genes: A B A+B
Length: 724 303 1000
Sequences: 545 68641 275
Seq/Len: 0.75 226.54 0.28
MirrorTree (Pazo et al. 2001) 0.06
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 0.03 0.19 0.02
2 0.03 0.21 0.04
5 0.04 0.24 0.11
10 0.04 0.27 0.17
20 0.04 0.29 0.27
100 0.04 0.33 0.49
∞ 0.05 0.34 0.54
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
473_V 162_A 1.35 0.31 0.00
229_E 112_L 1.15 0.21 0.00
378_R 266_E 1.12 0.20 0.00
633_P 18_G 1.11 0.19 0.00
182_I 127_G 1.11 0.19 0.00
181_V 289_A 1.09 0.18 0.00
515_E 146_I 1.09 0.18 0.00
514_T 197_M 1.08 0.18 0.00
437_L 95_H 1.04 0.16 0.00
89_T 18_G 1.02 0.16 0.00
295_D 288_R 1.01 0.15 0.00
63_S 127_G 1.01 0.15 0.00
167_V 130_F 1.00 0.15 0.00
635_V 149_T 1.00 0.15 0.00
288_I 34_L 1.00 0.15 0.00
185_L 279_N 1.00 0.15 0.00
437_L 24_R 0.98 0.14 0.00
474_S 127_G 0.98 0.14 0.00
147_T 276_L 0.95 0.14 0.00
585_V 162_A 0.95 0.13 0.00
67_S 128_L 0.94 0.13 0.00
529_D 104_L 0.94 0.13 0.00
147_T 213_L 0.93 0.13 0.00
380_V 198_W 0.93 0.13 0.00
297_T 281_H 0.93 0.13 0.00
380_V 226_I 0.92 0.12 0.00
528_F 122_R 0.92 0.12 0.00
86_L 281_H 0.91 0.12 0.00
698_E 6_Y 0.91 0.12 0.00
295_D 12_I 0.90 0.12 0.00
437_L 153_T 0.90 0.12 0.00
394_M 148_V 0.89 0.12 0.00
587_S 33_A 0.89 0.12 0.00
514_T 186_L 0.89 0.12 0.00
242_K 192_A 0.88 0.12 0.00
156_A 148_V 0.88 0.11 0.00
684_I 71_V 0.87 0.11 0.00
467_T 131_L 0.86 0.11 0.00
191_E 104_L 0.86 0.11 0.00
635_V 199_S 0.85 0.11 0.00
271_K 29_G 0.85 0.11 0.00
332_L 207_M 0.85 0.11 0.00
74_D 199_S 0.85 0.11 0.00
529_D 190_T 0.85 0.11 0.00
330_R 131_L 0.85 0.11 0.00
147_T 90_T 0.85 0.11 0.00
271_K 59_L 0.85 0.10 0.00
473_V 91_L 0.84 0.10 0.00
546_D 203_I 0.83 0.10 0.00
296_I 9_V 0.83 0.10 0.00
364_D 68_H 0.83 0.10 0.00
528_F 43_G 0.82 0.10 0.00
437_L 12_I 0.82 0.10 0.00
202_V 267_S 0.82 0.10 0.00
485_Y 12_I 0.82 0.10 0.00
563_L 18_G 0.82 0.10 0.00
11_E 271_L 0.82 0.10 0.00
246_E 92_V 0.81 0.10 0.00
75_I 23_A 0.81 0.10 0.00
674_Q 288_R 0.81 0.10 0.00
227_D 12_I 0.81 0.10 0.00
264_D 168_Q 0.81 0.10 0.00
181_V 194_P 0.81 0.10 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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