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OPENSEQ.org
cI_B_2_cIV_A_2_Pdenitr
Genes: A B A+B
Length: 175 539 672
Sequences: 1604 4455 957
Seq/Len: 9.17 8.27 1.42
MirrorTree (Pazo et al. 2001) 0.11
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 0.01 0.00
2 0.01 0.01 0.01
5 0.02 0.02 0.01
10 0.02 0.03 0.03
20 0.03 0.03 0.07
100 0.04 0.05 0.32
∞ 0.10 0.08 1.34
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
157_L 407_F 0.87 0.31 0.00
66_R 30_I 0.84 0.28 0.00
157_L 72_W 0.81 0.26 0.00
165_R 429_A 0.81 0.26 0.00
146_V 421_S 0.81 0.26 0.00
40_A 426_P 0.78 0.23 0.00
78_A 22_F 0.78 0.23 0.00
45_L 213_A 0.76 0.22 0.00
160_I 500_K 0.75 0.21 0.00
160_I 303_L 0.74 0.21 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
3486 1.25 cI_B_20_cIV_A_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3484 1.42 cI_B_2_cIV_A_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3483 1.4 cI_B_6_cIV_A_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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