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OPENSEQ.org
test-cua-pcua
Genes: A B A+B
Length: 135 120 238
Sequences: 2002 1183 359
Seq/Len: 14.83 9.86 1.51
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 0.01 0.00 0.00
2 0.01 0.00 0.01
5 0.01 0.01 0.06
10 0.01 0.01 0.09
20 0.02 0.01 0.11
100 0.02 0.01 0.23
∞ 0.09 0.06 1.41
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
72_F 3_F 1.06 0.51 0.00
94_V 26_G 0.76 0.23 0.00
66_Q 5_E 0.75 0.22 0.00
105_T 95_A 0.74 0.21 0.00
62_I 55_G 0.73 0.20 0.00
32_A 35_A 0.73 0.20 0.00
132_V 64_V 0.71 0.19 0.00
70_I 38_P 0.68 0.17 0.00
105_T 101_L 0.67 0.17 0.00
74_I 70_P 0.67 0.17 0.00
64_V 95_A 0.67 0.17 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
0772 1.51 test-cua-pcua Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done
0766 0.12 test-cua-pcua Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed - Shared
0765 0.02 test-cua-pcua Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
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