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OPENSEQ.org
CA-VC
Genes: A B A+B
Length: 81 112 191
Sequences: 19735 49194 12162
Seq/Len: 243.64 439.23 63.68
MirrorTree (Pazo et al. 2001) 0.87
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 0.02 63.02
2 0.02 0.04 65.37
5 0.04 0.06 67.99
10 0.05 0.09 70.59
20 0.08 0.13 73.21
100 0.16 0.22 83.82
∞ 0.23 0.26 89.78
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
52_R 12_N 0.53 0.32 0.00
47_D 8_Q 0.50 0.28 0.00
31_L 8_Q 0.44 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
5317 29.97 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
5310 63.68 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 1) msa: HHblits (2015_06) 0.00 Done
5256 29.91 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
5255 0.01 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
5254 0.01 CA-VC Δgene:(1, 1) A:(1E-40, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
5253 73.84 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
5252 0.01 CA-VC Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed
5251 80.51 CA-VC Δgene:(1, 1) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done
5250 75.52 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
5248 87.39 CA-VC Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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