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OPENSEQ.org
cIV_A_10_cI_K_10_Pdenitr
Genes: A B A+B
Length: 538 101 613
Sequences: 4448 4172 1821
Seq/Len: 8.27 41.31 2.97
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 0.00 0.03
2 0.01 0.00 0.05
5 0.02 0.01 0.17
10 0.02 0.01 0.95
20 0.03 0.01 1.04
100 0.04 0.03 1.43
∞ 0.08 0.07 2.85
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
438_I 29_V 1.01 0.65 0.01
410_A 34_M 0.87 0.49 0.01
196_M 34_M 0.87 0.48 0.01
282_A 9_V 0.78 0.38 0.00
124_C 36_I 0.78 0.37 0.00
29_I 30_I 0.77 0.37 0.00
196_M 82_V 0.77 0.36 0.00
486_F 30_I 0.77 0.36 0.00
486_F 99_M 0.74 0.33 0.00
96_G 66_V 0.74 0.33 0.00
507_W 60_Q 0.72 0.31 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
3364 2.98 cIV_A_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3362 2.97 cIV_A_10_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3359 3.4 cIV_A_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3358 3.42 cIV_A_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3356 0.36 cIV_A_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3355 3.6 cIV_A_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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