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OPENSEQ.org
1vs8_4_G
Genes: A B A+B
Length: 38 177 211
Sequences: 973 3374 1280
Seq/Len: 25.61 19.06 6.07
MirrorTree (Pazo et al. 2001) 0.54
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 0.10 0.08 0.00
2 0.10 0.08 0.00
5 0.10 0.08 0.45
10 0.10 0.08 5.66
20 0.10 0.08 5.95
100 0.10 0.08 6.16
∞ 0.12 0.09 7.22
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
31_P 170_R 1.52 0.99 0.87
15_K 63_A 0.72 0.49 0.17
21_G 74_S 0.67 0.41 0.13
9_K 118_P 0.67 0.41 0.13
28_S 168_V 0.65 0.39 0.12
32_K 35_R 0.63 0.36 0.11
22_V 6_K 0.62 0.35 0.10
18_K 144_V 0.61 0.33 0.10
15_K 38_N 0.61 0.33 0.10
18_K 104_N 0.60 0.32 0.09
9_K 59_A 0.59 0.31 0.09
24_R 165_A 0.59 0.31 0.09
20_D 124_E 0.59 0.31 0.09
16_I 106_S 0.59 0.30 0.09
15_K 80_T 0.59 0.30 0.09
35_Q 87_L 0.59 0.30 0.09
12_R 177_K 0.58 0.29 0.08
12_R 174_A 0.58 0.29 0.08
20_D 50_L 0.58 0.29 0.08
36_R 121_I 0.57 0.28 0.08
32_K 7_A 0.57 0.28 0.08
22_V 134_K 0.56 0.26 0.07
17_V 97_A 0.56 0.26 0.07
21_G 171_T 0.55 0.26 0.07
27_C 112_P 0.54 0.24 0.07
31_P 162_V 0.54 0.24 0.06
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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