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OPENSEQ.org
14Avs14B
Genes: A B A+B
Length: 125 110 225
Sequences: 4284 90 92
Seq/Len: 34.27 0.82 0.41
MirrorTree (Pazo et al. 2001) 0.16
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 0.07 0.01 0.00
2 0.10 0.01 0.01
5 0.10 0.01 0.01
10 0.11 0.01 0.01
20 0.12 0.01 0.05
100 0.14 0.01 0.13
∞ 0.19 0.01 0.39
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
84_N 45_I 1.40 0.43 0.00
65_E 9_I 1.30 0.36 0.00
19_R 94_S 1.21 0.30 0.00
48_I 74_E 1.13 0.26 0.00
72_N 45_I 0.99 0.19 0.00
32_A 10_F 0.95 0.17 0.00
91_Y 45_I 0.89 0.14 0.00
69_D 25_K 0.85 0.13 0.00
73_A 1_M 0.84 0.13 0.00
35_M 26_C 0.84 0.13 0.00
98_F 70_Y 0.83 0.12 0.00
108_E 62_G 0.82 0.12 0.00
84_N 26_C 0.80 0.12 0.00
11_I 103_K 0.79 0.11 0.00
103_T 24_E 0.79 0.11 0.00
109_Q 15_A 0.75 0.10 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
3987 0.36 14Avs14B_mk Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3902 0.65 14Avs14B_staszek Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3897 0.58 14Avs14B_staszek Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3896 0.33 lolo3_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3895 0.33 lolo3_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3894 0 lolo3 Δgene:(1, 5) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
3893 0.41 14Avs14B Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done
3879 0.58 14Avs14B Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3878 0.07 14Avs14B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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