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OPENSEQ.org
rrn5 hht1
Genes: A B A+B
Length: 101 136 226
Sequences: 2338 712 189
Seq/Len: 23.15 5.24 0.84
MirrorTree (Pazo et al. 2001) 0.08
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 0.05 0.05 0.01
2 0.05 0.06 0.02
5 0.06 0.07 0.03
10 0.06 0.08 0.05
20 0.07 0.08 0.09
100 0.10 0.09 0.28
∞ 0.15 0.12 0.80
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
58_A 90_I 1.08 0.37 0.00
44_S 88_S 0.90 0.23 0.00
25_L 43_K 0.89 0.23 0.00
59_S 42_Y 0.87 0.21 0.00
44_S 54_R 0.86 0.21 0.00
92_T 103_S 0.85 0.21 0.00
62_A 90_I 0.83 0.19 0.00
25_L 55_F 0.83 0.19 0.00
29_S 126_K 0.82 0.19 0.00
66_K 30_A 0.81 0.18 0.00
60_A 88_S 0.77 0.16 0.00
20_T 75_I 0.76 0.16 0.00
23_W 58_S 0.75 0.15 0.00
68_G 116_K 0.75 0.15 0.00
17_E 99_A 0.74 0.15 0.00
75_A 54_R 0.73 0.14 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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