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OPENSEQ.org
bolagrxd
Genes: A B A+B
Length: 105 115 209
Sequences: 1362 2782 592
Seq/Len: 12.97 24.19 2.83
MirrorTree (Pazo et al. 2001) 0.33
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 0.02 0.27
2 0.00 0.02 0.30
5 0.00 0.02 0.30
10 0.00 0.02 0.33
20 0.00 0.02 0.35
100 0.00 0.03 0.60
∞ 0.00 0.05 2.69
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
39_F 12_I 1.07 0.71 0.02
15_F 6_E 0.86 0.47 0.01
72_V 40_L 0.85 0.45 0.01
81_T 91_Y 0.79 0.38 0.01
53_F 98_Q 0.78 0.37 0.01
61_Y 67_N 0.78 0.36 0.01
60_I 107_Y 0.76 0.34 0.01
57_H 34_A 0.75 0.33 0.01
58_R 29_S 0.75 0.33 0.01
43_L 91_Y 0.74 0.32 0.01
72_V 46_R 0.74 0.32 0.01
81_T 101_K 0.73 0.32 0.01
43_L 54_Q 0.73 0.31 0.01
52_R 60_A 0.73 0.31 0.01
24_D 49_Y 0.72 0.30 0.01
53_F 81_V 0.72 0.30 0.01
32_P 45_E 0.72 0.30 0.01
77_L 34_A 0.72 0.30 0.01
61_Y 25_P 0.72 0.30 0.01
62_S 67_N 0.71 0.29 0.01
61_Y 104_A 0.70 0.28 0.01
60_I 60_A 0.69 0.27 0.01
57_H 42_A 0.69 0.27 0.01
49_T 47_F 0.69 0.27 0.01
50_G 44_G 0.67 0.25 0.01
8_E 78_G 0.67 0.25 0.01
45_S 81_V 0.66 0.24 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
2050 2.83 bolagrxd Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.02 Done - Shared
2037 1.82 bolagrxd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.02 Done - Shared
2036 0.11 bolagrx Δgene:(1, 5) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2015_03) Killed - Shared
1470 1.56 bolagrxd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.19 Done - Shared
1469 0.03 bolagrxd Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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