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OPENSEQ.org
D1A2OA1_D1A2OA2 hhblits 1e-20 8 1-20
Genes: A B A+B
Length: 124 183 298
Sequences: 76743 3447 2280
Seq/Len: 618.9 18.84 7.65
MirrorTree (Pazo et al. 2001) 0.38
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 0.05 3.08
2 0.13 0.05 3.92
5 0.16 0.06 5.41
10 0.18 0.06 6.89
20 0.22 0.06 7.43
100 0.31 0.08 8.71
∞ 0.34 0.18 9.17
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
102_V 59_D 0.58 0.34 0.00
2_R 29_I 0.55 0.29 0.00
50_L 19_Q 0.51 0.25 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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