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OPENSEQ.org
Javier
Genes: A B A+B
Length: 108 168 267
Sequences: 18247 8927 569
Seq/Len: 168.95 53.14 2.13
MirrorTree (Pazo et al. 2001) 0.22
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 0.02 0.01 0.20
2 0.03 0.01 0.39
5 0.03 0.01 0.72
10 0.04 0.02 1.25
20 0.05 0.03 2.06
100 0.10 0.06 6.11
∞ 0.20 0.17 14.01
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
72_I 49_V 0.89 0.41 0.00
100_K 46_K 0.85 0.38 0.00
83_N 144_V 0.85 0.37 0.00
43_D 137_V 0.83 0.35 0.00
23_I 144_V 0.81 0.34 0.00
53_L 24_K 0.78 0.30 0.00
58_L 100_L 0.78 0.30 0.00
71_G 29_T 0.77 0.29 0.00
60_I 85_A 0.76 0.28 0.00
64_P 141_N 0.75 0.28 0.00
103_L 153_I 0.75 0.28 0.00
25_V 141_N 0.74 0.27 0.00
25_V 20_Q 0.72 0.25 0.00
41_I 23_S 0.72 0.25 0.00
44_E 93_R 0.67 0.20 0.00
51_G 137_V 0.66 0.20 0.00
25_V 108_T 0.66 0.20 0.00
59_N 78_T 0.66 0.20 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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