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OPENSEQ.org
cardiac myosin vs MyBP-C C1
Genes: A B A+B
Length: 800 110 877
Sequences: 2708 15636 244
Seq/Len: 3.38 142.15 0.28
MirrorTree (Pazo et al. 2001) 0.08
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 0.15 0.01
2 0.06 0.18 0.01
5 0.06 0.20 0.02
10 0.06 0.22 0.05
20 0.07 0.24 0.07
100 0.09 0.27 0.19
∞ 0.12 0.28 0.27
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
390_L 16_V 1.56 0.44 0.00
349_M 48_D 1.14 0.20 0.00
506_I 54_G 1.04 0.17 0.00
343_S 22_I 0.99 0.15 0.00
670_V 74_L 0.98 0.14 0.00
443_I 42_F 0.98 0.14 0.00
155_F 31_A 0.98 0.14 0.00
717_D 22_I 0.98 0.14 0.00
69_V 39_V 0.94 0.13 0.00
193_Q 92_S 0.94 0.13 0.00
388_M 28_V 0.91 0.12 0.00
273_V 26_A 0.90 0.12 0.00
417_V 45_K 0.90 0.12 0.00
690_M 76_I 0.89 0.12 0.00
118_S 104_L 0.87 0.11 0.00
125_V 78_D 0.87 0.11 0.00
416_N 22_I 0.86 0.11 0.00
71_V 57_L 0.86 0.11 0.00
739_R 99_C 0.85 0.11 0.00
754_N 24_F 0.85 0.10 0.00
385_A 22_I 0.84 0.10 0.00
582_Y 87_Y 0.84 0.10 0.00
613_S 76_I 0.84 0.10 0.00
344_E 76_I 0.84 0.10 0.00
125_V 7_F 0.83 0.10 0.00
156_S 54_G 0.82 0.10 0.00
647_V 87_Y 0.82 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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