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OPENSEQ.org
rrn10 rrn5 (A, 60-110) (B, 1-65) (A, 25-51)
Genes: A B A+B
Length: 27 65 84
Sequences: 137 6303 60
Seq/Len: 5.07 96.97 0.71
MirrorTree (Pazo et al. 2001) 0.20
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 0.00 0.05 0.01
2 0.00 0.06 0.01
5 0.00 0.08 0.01
10 0.00 0.09 0.05
20 0.00 0.10 0.07
100 0.00 0.14 0.16
∞ 0.00 0.20 0.65
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
13_I 25_L 1.37 0.57 0.00
19_I 17_E 1.35 0.55 0.00
7_F 24_C 1.21 0.43 0.00
10_T 40_L 1.17 0.40 0.00
12_L 21_F 1.15 0.39 0.00
13_I 23_W 1.15 0.38 0.00
24_K 41_P 1.04 0.30 0.00
20_E 47_E 1.02 0.28 0.00
11_S 20_T 0.94 0.23 0.00
20_E 40_L 0.93 0.23 0.00
25_D 44_S 0.92 0.22 0.00
21_K 42_R 0.92 0.22 0.00
22_W 32_R 0.90 0.21 0.00
20_E 33_V 0.88 0.20 0.00
26_Y 19_N 0.85 0.18 0.00
1_P 36_W 0.85 0.18 0.00
23_V 27_R 0.85 0.18 0.00
20_E 17_E 0.84 0.18 0.00
7_F 27_R 0.84 0.18 0.00
27_L 22_F 0.83 0.17 0.00
8_D 13_W 0.81 0.16 0.00
9_E 46_M 0.80 0.16 0.00
27_L 36_W 0.79 0.16 0.00
20_E 55_L 0.79 0.15 0.00
16_G 24_C 0.79 0.15 0.00
21_K 38_S 0.78 0.15 0.00
14_T 19_N 0.77 0.15 0.00
10_T 11_V 0.76 0.14 0.00
5_N 41_P 0.74 0.13 0.00
26_Y 14_D 0.74 0.13 0.00
7_F 34_D 0.73 0.13 0.00
19_I 12_D 0.73 0.13 0.00
5_N 21_F 0.73 0.13 0.00
14_T 14_D 0.72 0.12 0.00
9_E 30_I 0.71 0.12 0.00
17_L 12_D 0.71 0.12 0.00
17_L 23_W 0.71 0.12 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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