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OPENSEQ.org
cIp_9_4_cIV_A_4
Genes: A B A+B
Length: 163 558 684
Sequences: 2843 4375 1199
Seq/Len: 17.44 7.84 1.75
MirrorTree (Pazo et al. 2001) 0.08
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 0.01 0.01
2 0.03 0.01 0.01
5 0.04 0.02 0.01
10 0.04 0.03 0.03
20 0.05 0.03 0.08
100 0.07 0.05 0.35
∞ 0.16 0.08 1.66
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
31_P 505_G 0.94 0.42 0.00
26_R 425_F 0.93 0.41 0.00
76_A 367_I 0.84 0.32 0.00
73_V 198_I 0.78 0.27 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
3681 1.75 cIp_9_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3680 0.67 cIp_9_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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