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OPENSEQ.org
qwe1 (B, 35-143)
Genes: A B A+B
Length: 208 109 307
Sequences: 2086 5430 1151
Seq/Len: 10.03 49.82 3.75
MirrorTree (Pazo et al. 2001) 0.16
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 0.00 0.07 0.00
2 0.00 0.07 0.01
5 0.00 0.08 0.03
10 0.00 0.08 0.04
20 0.00 0.09 0.20
100 0.01 0.11 0.81
∞ 0.06 0.22 3.63
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
23_F 60_D 0.71 0.35 0.00
66_Q 22_V 0.69 0.32 0.00
25_V 28_R 0.68 0.32 0.00
152_Q 39_S 0.66 0.29 0.00
160_V 41_N 0.63 0.26 0.00
28_I 99_A 0.61 0.24 0.00
88_I 53_G 0.60 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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