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OPENSEQ.org
Li
Genes: A B A+B
Length: 47 370 398
Sequences: 3629 7064 410
Seq/Len: 77.21 19.09 1.03
MirrorTree (Pazo et al. 2001) 0.10
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 0.09 0.04 0.00
2 0.10 0.04 0.01
5 0.11 0.04 0.04
10 0.12 0.05 0.06
20 0.13 0.05 0.13
100 0.18 0.08 0.40
∞ 0.23 0.17 0.98
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
36_D 97_R 1.21 0.54 0.00
30_I 245_I 1.20 0.53 0.00
34_S 321_E 1.09 0.42 0.00
6_D 141_V 1.07 0.41 0.00
15_I 252_M 1.07 0.41 0.00
24_R 21_D 1.01 0.36 0.00
1_R 338_A 0.97 0.32 0.00
37_Y 94_G 0.94 0.30 0.00
24_R 347_I 0.93 0.29 0.00
35_V 273_V 0.89 0.26 0.00
15_I 135_E 0.89 0.26 0.00
36_D 37_I 0.88 0.25 0.00
27_K 333_G 0.87 0.25 0.00
27_K 62_V 0.86 0.24 0.00
4_I 273_V 0.85 0.23 0.00
30_I 127_Y 0.84 0.23 0.00
4_I 338_A 0.84 0.23 0.00
27_K 336_R 0.81 0.21 0.00
10_E 129_D 0.79 0.20 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
13153 1.03 Li Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13152 0 Li Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
13151 0 Li Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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