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OPENSEQ.org
x265-f
Genes: A B A+B
Length: 265 228 476
Sequences: 7100 87698 1214
Seq/Len: 26.79 384.64 2.55
MirrorTree (Pazo et al. 2001) 0.07
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 0.02 0.10 0.04
2 0.03 0.11 0.12
5 0.04 0.15 0.62
10 0.05 0.20 1.33
20 0.07 0.25 2.46
100 0.10 0.36 7.11
∞ 0.18 0.38 8.95
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
61_A 47_T 0.83 0.40 0.00
58_V 6_V 0.79 0.35 0.00
252_V 164_I 0.71 0.27 0.00
110_I 180_Q 0.71 0.27 0.00
31_I 159_I 0.70 0.27 0.00
179_A 39_M 0.69 0.25 0.00
24_N 104_E 0.68 0.24 0.00
175_N 38_I 0.68 0.24 0.00
4_K 164_I 0.66 0.23 0.00
249_E 198_I 0.65 0.21 0.00
227_L 38_I 0.64 0.21 0.00
168_W 186_L 0.64 0.21 0.00
105_Q 9_L 0.63 0.20 0.00
68_A 188_R 0.63 0.20 0.00
147_E 198_I 0.63 0.20 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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