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OPENSEQ.org
2ns1_B_A
Genes: A B A+B
Length: 116 412 512
Sequences: 2551 4096 1452
Seq/Len: 21.99 9.94 2.84
MirrorTree (Pazo et al. 2001) 0.26
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.02 2.68
2 0.06 0.04 2.72
5 0.06 0.04 2.73
10 0.06 0.05 2.73
20 0.06 0.05 2.75
100 0.07 0.06 2.84
∞ 0.19 0.13 3.24
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
89_K 388_E 1.44 0.94 0.57
12_I 242_I 0.90 0.51 0.14
83_K 305_L 0.84 0.44 0.11
103_V 298_G 0.77 0.36 0.08
48_E 249_E 0.71 0.29 0.06
97_V 243_L 0.69 0.28 0.06
112_D 117_G 0.67 0.26 0.05
44_K 250_W 0.67 0.25 0.05
52_G 38_G 0.65 0.23 0.05
98_A 115_I 0.65 0.23 0.04
104_I 159_L 0.64 0.23 0.04
100_L 69_G 0.64 0.23 0.04
22_E 124_R 0.64 0.23 0.04
49_L 35_L 0.64 0.22 0.04
63_V 375_K 0.64 0.22 0.04
75_D 49_T 0.63 0.22 0.04
98_A 127_A 0.63 0.21 0.04
100_L 283_G 0.62 0.21 0.04
32_L 317_V 0.61 0.20 0.04
94_K 117_G 0.61 0.20 0.04
80_I 30_L 0.60 0.20 0.04
112_D 310_D 0.60 0.20 0.04
48_E 310_D 0.60 0.20 0.04
46_H 263_S 0.60 0.19 0.04
80_I 184_K 0.60 0.19 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)
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