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OPENSEQ.org
test4mdp
Genes: A B A+B
Length: 149 287 409
Sequences: 235 72162 74
Seq/Len: 1.58 251.44 0.18
MirrorTree (Pazo et al. 2001) 0.04
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 0.10 0.01
2 0.05 0.13 0.02
5 0.07 0.16 0.05
10 0.07 0.20 0.11
20 0.08 0.24 0.17
100 0.09 0.31 0.32
∞ 0.10 0.34 0.35
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
95_R 153_V 1.07 0.13 0.00
95_R 188_I 1.06 0.13 0.00
135_V 186_E 1.06 0.13 0.00
95_R 16_K 1.03 0.12 0.00
99_S 147_V 0.95 0.10 0.00
145_Q 198_D 0.95 0.10 0.00
127_Q 71_V 0.91 0.10 0.00
145_Q 203_G 0.88 0.09 0.00
149_R 79_L 0.87 0.09 0.00
95_R 268_S 0.86 0.09 0.00
135_V 185_L 0.84 0.08 0.00
95_R 160_L 0.84 0.08 0.00
78_E 90_L 0.83 0.08 0.00
95_R 102_D 0.83 0.08 0.00
64_R 257_S 0.80 0.08 0.00
74_A 157_D 0.79 0.07 0.00
119_T 136_V 0.79 0.07 0.00
113_L 37_G 0.79 0.07 0.00
135_V 184_A 0.78 0.07 0.00
74_A 145_V 0.78 0.07 0.00
125_I 147_V 0.78 0.07 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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