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OPENSEQ.org
2trx
Genes: A B A+B
Length: 108 351 414
Sequences: 9986 9978 1237
Seq/Len: 92.46 28.43 2.99
MirrorTree (Pazo et al. 2001) 0.06
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 0.02 0.04 0.03
2 0.02 0.05 0.07
5 0.02 0.07 0.13
10 0.03 0.09 0.29
20 0.03 0.14 0.56
100 0.07 0.26 1.75
∞ 0.19 0.32 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
101_E 156_I 1.02 0.66 0.01
71_G 205_V 0.77 0.37 0.01
44_E 37_L 0.71 0.30 0.00
48_E 296_E 0.67 0.26 0.00
65_G 130_Y 0.65 0.24 0.00
11_S 261_K 0.64 0.23 0.00
42_L 281_L 0.64 0.23 0.00
67_A 284_M 0.64 0.23 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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