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OPENSEQ.org
rrn5 hhf1
Genes: A B A+B
Length: 101 103 193
Sequences: 2338 758 252
Seq/Len: 23.15 7.36 1.31
MirrorTree (Pazo et al. 2001) -0.01
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 0.05 0.01
5 0.06 0.06 0.03
10 0.06 0.06 0.05
20 0.07 0.07 0.17
100 0.10 0.12 0.43
∞ 0.15 0.16 1.24
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
14_D 53_E 0.99 0.39 0.00
55_L 42_G 0.96 0.36 0.00
28_Y 50_L 0.84 0.27 0.00
19_N 25_D 0.82 0.25 0.00
89_L 66_V 0.81 0.24 0.00
19_N 76_H 0.78 0.22 0.00
39_L 63_L 0.76 0.21 0.00
61_S 70_S 0.75 0.20 0.00
47_E 70_S 0.74 0.20 0.00
88_K 87_V 0.73 0.19 0.00
69_D 49_G 0.73 0.19 0.00
83_V 70_S 0.72 0.18 0.00
12_D 70_S 0.72 0.18 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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