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OPENSEQ.org
cardiac myosin vs MyBP-C C3_real
Genes: A B A+B
Length: 800 92 860
Sequences: 2708 18632 252
Seq/Len: 3.38 202.52 0.29
MirrorTree (Pazo et al. 2001) 0.05
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.16 0.01
2 0.06 0.19 0.01
5 0.06 0.21 0.02
10 0.06 0.23 0.05
20 0.07 0.25 0.08
100 0.09 0.28 0.21
∞ 0.12 0.29 0.28
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
353_T 63_I 1.18 0.23 0.00
537_E 42_L 1.04 0.17 0.00
154_I 60_H 1.00 0.15 0.00
756_Y 22_F 0.99 0.15 0.00
468_F 80_G 0.99 0.15 0.00
69_V 33_V 0.98 0.15 0.00
457_I 81_G 0.96 0.14 0.00
476_L 14_V 0.96 0.14 0.00
536_E 22_F 0.94 0.14 0.00
786_T 42_L 0.93 0.13 0.00
718_F 24_C 0.93 0.13 0.00
430_A 42_L 0.92 0.13 0.00
293_K 26_V 0.92 0.13 0.00
592_G 14_V 0.90 0.12 0.00
763_V 12_Q 0.89 0.12 0.00
338_V 63_I 0.89 0.12 0.00
342_T 56_G 0.88 0.12 0.00
339_L 63_I 0.88 0.12 0.00
428_A 29_E 0.86 0.11 0.00
229_A 9_L 0.86 0.11 0.00
716_G 26_V 0.86 0.11 0.00
399_L 67_M 0.85 0.11 0.00
125_V 55_D 0.84 0.10 0.00
341_F 17_G 0.84 0.10 0.00
298_L 80_G 0.83 0.10 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)
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