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OPENSEQ.org
cIV_A_4_cI_M_20_1_Pdenitr
Genes: A B A+B
Length: 538 513 1006
Sequences: 4477 5240 1989
Seq/Len: 8.32 10.21 1.98
MirrorTree (Pazo et al. 2001) 0.33
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 0.06 0.02
2 0.01 0.06 0.05
5 0.02 0.07 0.12
10 0.03 0.08 0.64
20 0.03 0.08 0.72
100 0.05 0.09 0.94
∞ 0.08 0.12 1.89
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
378_S 94_F 1.32 0.82 0.09
378_S 50_L 0.86 0.37 0.02
24_G 318_V 0.82 0.33 0.02
301_I 477_V 0.80 0.31 0.02
273_I 238_V 0.79 0.30 0.01
172_V 307_S 0.79 0.30 0.01
343_I 252_A 0.79 0.29 0.01
67_N 375_L 0.79 0.29 0.01
175_A 411_G 0.78 0.29 0.01
361_F 318_V 0.74 0.26 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
3340 1.98 cIV_A_6_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3339 1.66 cIV_A_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3328 1.98 cIV_A_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3327 2.23 cIV_A_4_cI_M_4_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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