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OPENSEQ.org
cardiac myosin vs MyBP-C C4
Genes: A B A+B
Length: 800 87 852
Sequences: 2708 21859 269
Seq/Len: 3.38 251.25 0.32
MirrorTree (Pazo et al. 2001) 0.06
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 0.17 0.01
2 0.06 0.19 0.01
5 0.06 0.22 0.02
10 0.06 0.24 0.05
20 0.07 0.26 0.09
100 0.09 0.29 0.24
∞ 0.12 0.30 0.30
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 21_F 1.13 0.22 0.00
182_A 77_G 1.08 0.20 0.00
428_A 10_D 1.07 0.19 0.00
154_I 9_A 1.04 0.18 0.00
105_L 21_F 1.02 0.17 0.00
431_V 16_K 1.02 0.17 0.00
718_F 23_C 1.01 0.17 0.00
385_A 27_D 0.99 0.16 0.00
349_M 30_V 0.99 0.16 0.00
685_D 21_F 0.99 0.16 0.00
459_V 77_G 0.98 0.16 0.00
335_A 27_D 0.97 0.15 0.00
418_Q 21_F 0.97 0.15 0.00
480_F 60_I 0.97 0.15 0.00
548_F 15_A 0.95 0.15 0.00
154_I 67_D 0.91 0.13 0.00
294_K 21_F 0.89 0.13 0.00
362_M 38_G 0.87 0.12 0.00
742_A 32_G 0.87 0.12 0.00
195_F 69_A 0.86 0.12 0.00
656_N 27_D 0.86 0.12 0.00
194_Y 32_G 0.86 0.12 0.00
746_L 37_N 0.83 0.11 0.00
647_V 71_Y 0.82 0.11 0.00
581_H 71_Y 0.82 0.11 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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