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OPENSEQ.org
S-F2
Genes: A B A+B
Length: 239 228 460
Sequences: 992 83932 999
Seq/Len: 4.15 368.12 2.17
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 0.01 0.10 0.65
2 0.01 0.11 0.81
5 0.01 0.14 1.02
10 0.01 0.19 1.21
20 0.02 0.25 1.48
100 0.04 0.35 2.02
∞ 0.11 0.37 2.14
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
63_E 26_I 0.81 0.34 0.00
156_G 58_Y 0.79 0.32 0.00
149_E 191_E 0.76 0.29 0.00
153_I 27_N 0.72 0.25 0.00
231_R 47_T 0.70 0.23 0.00
17_V 198_I 0.69 0.23 0.00
58_Q 4_L 0.69 0.22 0.00
168_I 54_S 0.68 0.22 0.00
218_L 32_E 0.66 0.21 0.00
199_S 87_I 0.65 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)
ID Seq/Len Name Options I_Prob Status
11248 26.51 S-F3 Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11247 2.17 S-F2 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11246 64.17 S-F1 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11213 41.34 S-F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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