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OPENSEQ.org
Phil - truncated
Genes: A B A+B
Length: 86 161 244
Sequences: 17115 19449 307
Seq/Len: 199.01 120.8 1.26
MirrorTree (Pazo et al. 2001) 0.13
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 0.13 0.07
2 0.03 0.16 0.12
5 0.06 0.18 0.21
10 0.08 0.19 0.32
20 0.10 0.21 0.50
100 0.15 0.24 0.93
∞ 0.21 0.25 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
75_N 106_V 0.93 0.33 0.00
66_E 138_I 0.90 0.30 0.00
76_P 93_S 0.83 0.25 0.00
68_I 94_S 0.78 0.22 0.00
69_G 53_E 0.75 0.20 0.00
78_M 88_K 0.75 0.20 0.00
51_V 90_F 0.74 0.19 0.00
18_V 24_Y 0.74 0.19 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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