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OPENSEQ.org
Adrian
Genes: A B A+B
Length: 302 308 559
Sequences: 64082 7355 3327
Seq/Len: 212.19 23.88 5.95
MirrorTree (Pazo et al. 2001) 0.12
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 0.06 0.57
2 0.12 0.07 0.75
5 0.16 0.08 1.26
10 0.19 0.08 1.93
20 0.23 0.09 2.82
100 0.31 0.14 4.94
∞ 0.33 0.19 5.45
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
158_M 184_Q 0.65 0.38 0.00
278_D 253_L 0.62 0.34 0.00
170_T 24_S 0.61 0.32 0.00
280_E 135_G 0.58 0.29 0.00
32_A 54_L 0.57 0.27 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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