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OPENSEQ.org
test
Genes: A B A+B
Length: 377 120 431
Sequences: 3433 1723 671
Seq/Len: 9.11 14.36 1.56
MirrorTree (Pazo et al. 2001) 0.42
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 0.02 0.00 0.00
2 0.03 0.00 0.00
5 0.06 0.00 0.00
10 0.06 0.00 0.01
20 0.07 0.00 0.03
100 0.08 0.00 0.15
∞ 0.14 0.00 1.35
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
260_V 93_I 1.07 0.53 0.00
85_E 61_A 1.03 0.49 0.00
229_V 24_V 1.02 0.47 0.00
236_Q 105_S 0.96 0.41 0.00
154_Y 97_I 0.92 0.37 0.00
230_P 7_Y 0.91 0.36 0.00
200_L 109_G 0.91 0.36 0.00
293_Q 54_V 0.88 0.34 0.00
66_E 9_V 0.82 0.28 0.00
116_G 30_V 0.80 0.26 0.00
132_K 52_S 0.78 0.25 0.00
129_G 45_A 0.78 0.25 0.00
204_S 8_K 0.77 0.24 0.00
65_E 117_K 0.77 0.24 0.00
79_L 54_V 0.76 0.23 0.00
174_Y 29_L 0.74 0.22 0.00
29_D 105_S 0.73 0.21 0.00
73_D 46_F 0.73 0.21 0.00
147_D 97_I 0.72 0.20 0.00
64_M 54_V 0.72 0.20 0.00
26_S 106_V 0.72 0.20 0.00
35_P 97_I 0.71 0.20 0.00
266_A 33_K 0.69 0.18 0.00
205_P 95_R 0.69 0.18 0.00
79_L 102_Q 0.68 0.18 0.00
51_H 93_I 0.67 0.17 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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