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OPENSEQ.org
DesKR
Genes: A B A+B
Length: 370 199 552
Sequences: 17042 39326 9970
Seq/Len: 46.06 197.62 18.06
MirrorTree (Pazo et al. 2001) 0.82
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.01 15.04
2 0.01 0.02 15.53
5 0.03 0.06 16.07
10 0.04 0.09 16.64
20 0.05 0.12 17.52
100 0.11 0.23 20.43
∞ 0.17 0.29 21.76
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
196_S 13_L 1.62 1.00 0.93
207_K 24_E 1.52 1.00 0.90
218_R 15_G 1.50 1.00 0.89
200_L 16_A 1.49 1.00 0.89
215_Q 22_N 1.20 0.98 0.71
204_L 20_L 1.16 0.97 0.67
203_D 105_P 1.14 0.97 0.66
211_K 25_D 1.09 0.96 0.60
203_D 106_S 1.07 0.95 0.59
207_K 107_E 1.06 0.95 0.57
200_L 17_L 0.98 0.91 0.48
207_K 23_L 0.95 0.89 0.44
222_S 15_G 0.92 0.87 0.41
235_R 103_D 0.91 0.86 0.39
208_L 23_L 0.89 0.85 0.37
226_T 12_M 0.89 0.85 0.37
197_L 13_L 0.85 0.81 0.33
219_E 19_S 0.80 0.76 0.28
225_Q 12_M 0.80 0.75 0.27
197_L 10_Q 0.79 0.73 0.26
197_L 12_M 0.77 0.71 0.24
222_S 12_M 0.69 0.59 0.17
228_R 105_P 0.66 0.54 0.15
193_Q 10_Q 0.65 0.51 0.14
193_Q 81_T 0.64 0.51 0.14
215_Q 19_S 0.61 0.46 0.12
200_L 13_L 0.55 0.36 0.08
204_L 19_S 0.54 0.34 0.08
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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