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OPENSEQ.org
cardiac myosin vs MyBP-C C0
Genes: A B A+B
Length: 800 96 859
Sequences: 2708 14332 233
Seq/Len: 3.38 149.29 0.27
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 0.15 0.00
2 0.06 0.17 0.01
5 0.06 0.20 0.02
10 0.06 0.22 0.04
20 0.07 0.23 0.07
100 0.09 0.26 0.19
∞ 0.12 0.27 0.26
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
385_A 29_F 1.35 0.30 0.00
459_V 85_S 1.25 0.25 0.00
766_K 75_D 1.15 0.20 0.00
746_L 33_T 1.09 0.18 0.00
349_M 54_K 1.06 0.17 0.00
394_D 83_A 1.05 0.17 0.00
352_L 67_T 1.03 0.16 0.00
715_Y 92_L 1.03 0.16 0.00
384_S 21_V 0.99 0.14 0.00
505_G 81_V 0.98 0.14 0.00
216_L 46_G 0.97 0.14 0.00
793_R 81_V 0.96 0.13 0.00
609_Y 34_E 0.96 0.13 0.00
354_G 20_E 0.95 0.13 0.00
505_G 68_V 0.93 0.12 0.00
609_Y 40_V 0.91 0.12 0.00
390_L 29_F 0.90 0.12 0.00
751_I 75_D 0.90 0.12 0.00
709_F 14_K 0.90 0.12 0.00
295_P 57_L 0.89 0.11 0.00
356_I 50_S 0.89 0.11 0.00
342_T 11_A 0.89 0.11 0.00
533_I 15_K 0.88 0.11 0.00
547_T 28_V 0.88 0.11 0.00
613_S 54_K 0.87 0.11 0.00
537_E 49_I 0.87 0.11 0.00
162_Y 36_A 0.87 0.11 0.00
579_L 78_S 0.87 0.11 0.00
106_K 16_P 0.86 0.11 0.00
158_S 74_A 0.86 0.11 0.00
533_I 12_F 0.85 0.10 0.00
504_E 66_L 0.85 0.10 0.00
614_L 16_P 0.84 0.10 0.00
154_I 17_R 0.84 0.10 0.00
154_I 42_W 0.84 0.10 0.00
319_T 77_G 0.84 0.10 0.00
285_I 19_V 0.83 0.10 0.00
158_S 43_Q 0.83 0.10 0.00
408_N 49_I 0.83 0.10 0.00
443_I 57_L 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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