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OPENSEQ.org
cardiac myosin vs MyBP-C C2
Genes: A B A+B
Length: 800 94 861
Sequences: 2708 11508 208
Seq/Len: 3.38 122.43 0.24
MirrorTree (Pazo et al. 2001) 0.04
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 0.14 0.00
2 0.06 0.16 0.00
5 0.06 0.18 0.01
10 0.06 0.20 0.03
20 0.07 0.22 0.04
100 0.09 0.25 0.15
∞ 0.12 0.26 0.23
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
742_A 37_V 1.35 0.28 0.00
742_A 18_V 1.08 0.16 0.00
423_A 53_Y 1.03 0.15 0.00
289_I 66_I 1.01 0.14 0.00
229_A 6_T 1.00 0.14 0.00
93_L 77_Y 1.00 0.14 0.00
339_L 79_C 1.00 0.14 0.00
531_M 26_L 0.99 0.14 0.00
763_V 16_Y 0.98 0.13 0.00
484_K 69_C 0.96 0.13 0.00
95_F 37_V 0.96 0.12 0.00
157_I 27_T 0.96 0.12 0.00
670_V 28_V 0.95 0.12 0.00
728_A 66_I 0.95 0.12 0.00
486_Q 18_V 0.94 0.12 0.00
681_P 66_I 0.93 0.12 0.00
384_S 37_V 0.92 0.12 0.00
355_A 28_V 0.92 0.12 0.00
377_G 90_L 0.92 0.11 0.00
648_S 42_N 0.91 0.11 0.00
786_T 69_C 0.90 0.11 0.00
76_V 46_I 0.89 0.11 0.00
144_G 48_M 0.88 0.11 0.00
536_E 81_V 0.88 0.11 0.00
386_Y 5_S 0.88 0.10 0.00
709_F 13_E 0.88 0.10 0.00
218_D 66_I 0.87 0.10 0.00
725_L 18_V 0.86 0.10 0.00
550_A 77_Y 0.86 0.10 0.00
98_E 73_D 0.86 0.10 0.00
307_P 81_V 0.85 0.10 0.00
344_E 90_L 0.85 0.10 0.00
395_L 29_E 0.85 0.10 0.00
171_N 77_Y 0.85 0.10 0.00
289_I 41_K 0.85 0.10 0.00
115_Y 66_I 0.84 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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