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OPENSEQ.org
cIV_A_20_cI_M_20_1_human
Genes: A B A+B
Length: 513 459 966
Sequences: 4412 4674 2656
Seq/Len: 8.6 10.18 2.75
MirrorTree (Pazo et al. 2001) 0.49
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 0.08
5 0.02 0.00 0.26
10 0.02 0.01 1.78
20 0.03 0.01 1.87
100 0.04 0.01 2.00
∞ 0.08 0.02 2.73
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
229_I 410_M 1.09 0.72 0.02
265_K 250_L 1.06 0.68 0.02
391_G 195_M 1.04 0.66 0.02
87_I 264_L 1.00 0.62 0.01
57_I 84_L 0.95 0.56 0.01
505_F 336_R 0.93 0.54 0.01
325_A 315_L 0.91 0.51 0.01
428_Q 285_L 0.88 0.48 0.01
318_V 164_L 0.88 0.47 0.01
330_S 270_I 0.87 0.46 0.01
356_I 150_L 0.87 0.46 0.01
169_I 285_L 0.86 0.45 0.01
31_T 278_R 0.86 0.45 0.01
159_L 377_G 0.84 0.43 0.01
198_S 291_I 0.84 0.42 0.01
338_V 202_A 0.83 0.42 0.01
426_F 221_V 0.82 0.41 0.01
415_T 39_L 0.82 0.41 0.01
395_H 121_F 0.81 0.40 0.01
413_H 413_T 0.81 0.39 0.01
12_H 239_G 0.81 0.39 0.01
475_A 226_A 0.81 0.39 0.01
482_V 252_P 0.81 0.39 0.01
334_W 35_S 0.80 0.38 0.01
189_L 210_Y 0.79 0.37 0.01
466_M 163_A 0.79 0.37 0.01
7_L 67_M 0.79 0.37 0.01
56_V 377_G 0.79 0.37 0.01
324_L 226_A 0.79 0.36 0.01
220_F 148_Y 0.78 0.36 0.01
69_M 328_C 0.78 0.36 0.01
492_L 252_P 0.78 0.36 0.01
461_S 285_L 0.78 0.35 0.01
362_S 218_K 0.77 0.35 0.01
407_Q 42_F 0.77 0.35 0.01
391_G 30_H 0.77 0.35 0.01
189_L 445_L 0.77 0.34 0.01
464_A 201_M 0.77 0.34 0.01
193_I 395_L 0.77 0.34 0.01
85_L 66_L 0.76 0.34 0.01
331_N 368_A 0.76 0.34 0.01
501_P 368_A 0.76 0.34 0.01
509_V 382_L 0.75 0.33 0.01
509_V 352_L 0.75 0.33 0.01
500_P 336_R 0.75 0.33 0.01
108_S 386_F 0.75 0.33 0.01
185_V 119_Y 0.75 0.33 0.01
419_I 243_M 0.75 0.32 0.01
45_G 266_L 0.75 0.32 0.01
403_Y 39_L 0.74 0.32 0.01
159_L 304_Q 0.74 0.32 0.01
177_T 52_C 0.74 0.31 0.01
117_M 264_L 0.73 0.31 0.01
168_I 346_Q 0.73 0.31 0.01
328_H 304_Q 0.73 0.30 0.01
172_K 140_P 0.72 0.30 0.01
155_V 435_T 0.72 0.30 0.01
278_M 406_Y 0.72 0.30 0.01
166_T 435_T 0.72 0.29 0.01
511_M 108_M 0.72 0.29 0.01
476_F 197_L 0.71 0.29 0.01
175_A 295_A 0.71 0.29 0.01
253_M 424_N 0.71 0.29 0.01
359_A 309_F 0.71 0.28 0.01
69_M 385_T 0.71 0.28 0.01
106_P 278_R 0.71 0.28 0.01
359_A 71_W 0.70 0.28 0.01
35_L 243_M 0.70 0.28 0.01
404_T 317_I 0.70 0.28 0.01
262_S 441_L 0.70 0.28 0.01
258_V 286_I 0.70 0.28 0.01
286_I 250_L 0.70 0.28 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
4418 1.62 cIV_A_80_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4416 1.15 cIV_A_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4415 1.17 cIV_A_80_1_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 1) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4414 1.15 cIV_A_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4413 1.62 cIV_A_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.17 Done - Shared
4408 2.75 cIV_A_20_cI_M_20_1_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4405 3.06 cIV_A_4_cI_M_4_1_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4398 2.38 cIV_A_40_cI_M_40_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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