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OPENSEQ.org
Ssp2 - Smk1
Genes: A B A+B
Length: 210 388 524
Sequences: 4191 9279 1831
Seq/Len: 19.96 23.91 3.49
MirrorTree (Pazo et al. 2001) 0.04
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 0.22 0.07 0.02
2 0.22 0.07 0.04
5 0.23 0.08 0.10
10 0.23 0.10 0.22
20 0.23 0.13 0.46
100 0.25 0.19 1.56
∞ 0.29 0.26 3.06
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
152_I 333_S 0.94 0.62 0.01
135_D 153_G 0.83 0.49 0.00
36_Y 233_I 0.78 0.41 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
7338 3.49 Ssp2 - Smk1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
7337 0.06 Ssp2 - Smk1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
7335 0 Ssp2 - Smk1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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