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OPENSEQ.org
cI_A_cIII_isp_human
Genes: A B A+B
Length: 115 82 188
Sequences: 4153 7597 951
Seq/Len: 36.11 92.65 5.06
MirrorTree (Pazo et al. 2001) 0.08
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 0.00 0.05 0.01
2 0.00 0.07 0.01
5 0.00 0.08 0.05
10 0.00 0.08 0.05
20 0.00 0.09 0.19
100 0.01 0.12 0.90
∞ 0.01 0.16 4.83
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
20_I 74_T 0.78 0.52 0.00
97_I 68_V 0.76 0.50 0.00
107_L 67_E 0.71 0.42 0.00
89_M 76_D 0.70 0.41 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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