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OPENSEQ.org
xs
Genes: A B A+B
Length: 307 239 498
Sequences: 1803 56493 944
Seq/Len: 5.87 236.37 1.9
MirrorTree (Pazo et al. 2001) 0.19
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 0.03 0.03 0.00
2 0.03 0.04 0.05
5 0.03 0.07 0.11
10 0.03 0.10 0.27
20 0.03 0.14 0.45
100 0.03 0.23 1.09
∞ 0.08 0.28 1.73
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
48_I 218_L 0.73 0.24 0.00
65_I 202_M 0.73 0.24 0.00
28_L 183_I 0.73 0.24 0.00
5_V 218_L 0.72 0.23 0.00
100_A 94_L 0.72 0.23 0.00
56_E 79_R 0.71 0.23 0.00
120_E 136_I 0.71 0.22 0.00
110_I 18_E 0.71 0.22 0.00
99_R 41_V 0.71 0.22 0.00
60_A 215_G 0.71 0.22 0.00
68_A 231_R 0.70 0.22 0.00
61_A 210_V 0.69 0.21 0.00
107_K 102_I 0.69 0.21 0.00
66_D 207_V 0.68 0.20 0.00
258_Y 34_V 0.68 0.20 0.00
5_V 173_R 0.68 0.20 0.00
199_K 113_G 0.68 0.20 0.00
247_I 168_I 0.66 0.19 0.00
148_L 44_M 0.66 0.19 0.00
60_A 207_V 0.66 0.19 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)
ID Seq/Len Name Options I_Prob Status
13438 0.29 xs-1 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13437 1.9 xs Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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