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OPENSEQ.org
cIV_A_60_cI_K_10_human
Genes: A B A+B
Length: 513 98 608
Sequences: 3040 3525 1511
Seq/Len: 5.93 35.97 2.49
MirrorTree (Pazo et al. 2001) 0.24
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 0.00 0.00 0.03
2 0.00 0.00 0.07
5 0.01 0.00 0.26
10 0.01 0.00 1.36
20 0.01 0.00 1.42
100 0.02 0.01 1.54
∞ 0.05 0.02 2.47
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
85_L 96_L 1.11 0.71 0.02
401_S 20_L 1.04 0.63 0.01
274_V 18_G 0.99 0.58 0.01
229_I 8_I 0.97 0.56 0.01
327_L 96_L 0.96 0.54 0.01
416_I 14_I 0.96 0.54 0.01
314_I 21_V 0.95 0.54 0.01
23_G 28_S 0.95 0.54 0.01
395_H 45_T 0.94 0.53 0.01
42_G 24_S 0.92 0.50 0.01
460_I 10_L 0.89 0.46 0.01
359_A 8_I 0.89 0.46 0.01
430_F 86_G 0.87 0.44 0.01
168_I 57_N 0.87 0.43 0.01
447_Y 36_M 0.86 0.42 0.01
342_L 96_L 0.86 0.42 0.01
423_L 6_M 0.85 0.41 0.01
462_L 39_S 0.84 0.41 0.01
133_A 98_C 0.83 0.39 0.01
277_M 64_L 0.83 0.39 0.01
70_V 97_Q 0.82 0.38 0.01
389_I 77_L 0.81 0.37 0.01
169_I 73_V 0.81 0.37 0.01
289_A 68_A 0.81 0.37 0.01
24_A 60_P 0.80 0.36 0.01
375_A 16_L 0.80 0.36 0.01
505_F 71_A 0.80 0.35 0.01
176_M 31_L 0.77 0.33 0.01
231_Y 72_A 0.77 0.32 0.01
100_M 69_C 0.76 0.32 0.01
362_S 26_L 0.76 0.32 0.01
464_A 14_I 0.76 0.32 0.01
464_A 96_L 0.76 0.31 0.01
353_L 32_C 0.75 0.30 0.01
361_S 77_L 0.75 0.30 0.01
392_G 39_S 0.75 0.30 0.01
357_V 48_T 0.75 0.30 0.01
117_M 14_I 0.75 0.30 0.01
204_A 77_L 0.75 0.30 0.01
216_N 9_M 0.74 0.30 0.01
118_V 23_R 0.74 0.30 0.01
215_L 53_S 0.74 0.29 0.01
392_G 97_Q 0.73 0.29 0.01
330_S 35_G 0.73 0.29 0.01
257_I 32_C 0.72 0.28 0.01
328_H 76_A 0.72 0.28 0.01
469_I 39_S 0.72 0.27 0.01
168_I 8_I 0.71 0.27 0.01
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
4519 2.81 cIV_A_20_cI_K_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4518 2.49 cIV_A_60_cI_K_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4517 2.53 cIV_A_40_cI_K_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4516 0.33 cIV_A_40_cI_K_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4515 0.03 cIV_A_40_cI_K_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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