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OPENSEQ.org
cIV_A_2_cI_J_2_Pdenitr
Genes: A B A+B
Length: 538 200 691
Sequences: 4476 6585 2747
Seq/Len: 8.32 32.92 3.98
MirrorTree (Pazo et al. 2001) 0.27
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 0.02
2 0.01 0.00 0.06
5 0.02 0.01 0.26
10 0.03 0.01 1.93
20 0.03 0.01 2.04
100 0.05 0.03 2.37
∞ 0.08 0.06 3.72
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
5_R 60_Y 1.18 0.88 0.15
438_I 21_V 1.07 0.79 0.11
26_V 161_A 0.96 0.69 0.08
442_L 48_G 0.94 0.66 0.07
305_V 62_G 0.89 0.60 0.06
531_P 33_L 0.89 0.60 0.06
351_I 105_G 0.87 0.58 0.06
249_V 8_L 0.86 0.56 0.06
376_V 66_V 0.85 0.55 0.05
507_W 49_A 0.85 0.54 0.05
159_A 156_V 0.84 0.53 0.05
131_A 43_L 0.83 0.52 0.05
278_I 161_A 0.81 0.50 0.05
200_K 25_N 0.81 0.50 0.05
501_V 150_A 0.81 0.49 0.04
42_Q 21_V 0.80 0.48 0.04
326_L 33_L 0.78 0.46 0.04
172_V 66_V 0.78 0.46 0.04
384_R 155_L 0.77 0.44 0.04
475_I 144_V 0.77 0.44 0.04
127_A 38_L 0.77 0.44 0.04
5_R 74_M 0.77 0.43 0.04
196_M 104_L 0.76 0.42 0.04
410_A 41_A 0.76 0.42 0.04
23_A 47_Q 0.75 0.41 0.04
530_L 101_L 0.74 0.41 0.04
485_L 21_V 0.73 0.39 0.03
378_S 5_A 0.73 0.38 0.03
286_I 152_L 0.72 0.38 0.03
22_T 62_G 0.72 0.38 0.03
74_M 9_F 0.72 0.38 0.03
99_F 158_M 0.72 0.37 0.03
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
3468 3.07 cIV_A_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.58 Done - Shared
3385 1.55 cIV_A_6_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3384 3.98 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3380 3.97 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3378 3.98 cIV_A_10_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3377 3.07 cIV_A_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3372 3.08 cIV_A_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.67 Done - Shared
3370 3.98 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3369 3.99 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
3368 0.61 cIV_A_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3367 4 cIV_A_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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