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DNAN_DPO3B_SALTY-UMUD_SALTY Jackhammer

Genes: A B A+B
Length: 366 139 493
Sequences: 7006 7987 1954
Seq/Len: 19.14 57.46 3.96
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.03
20 0.00 0.01 0.10
100 0.00 0.02 0.45
0.01 0.05 3.87
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
324_V 132_T 0.93 0.65 0.01
326_D 32_D 0.87 0.57 0.01
6_E 124_T 0.84 0.53 0.01
336_V 135_I 0.78 0.45 0.00
115_D 127_I 0.71 0.36 0.00
163_E 127_I 0.70 0.35 0.00
99_V 62_I 0.69 0.34 0.00
306_L 36_Q 0.68 0.32 0.00
324_V 55_K 0.66 0.31 0.00
204_M 56_A 0.66 0.31 0.00
76_F 59_D 0.66 0.30 0.00
61_Q 17_F 0.66 0.30 0.00
257_E 134_I 0.65 0.29 0.00
99_V 109_P 0.65 0.29 0.00
140_E 101_L 0.65 0.29 0.00
261_D 48_P 0.64 0.28 0.00
128_F 91_E 0.64 0.28 0.00
248_L 110_M 0.64 0.28 0.00
129_T 63_E 0.63 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
7083 3.96 DNAN_DPO3B_SALTY-UMUD_SALTY Jackhammer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
6892 0.1 DNAN_DPO3B_SALTY-UMUD_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared

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