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OPENSEQ.org
1b-N brute
Genes: A B A+B
Length: 20 844 749
Sequences: 127 388 84
Seq/Len: 6.35 0.46 0.11
MirrorTree (Pazo et al. 2001) 0.79
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.01
∞ 0.00 0.00 0.10
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
2_P 487_M 1.44 0.20 0.00
4_P 579_N 1.12 0.11 0.00
13_E 449_A 1.12 0.11 0.00
19_P 763_I 1.07 0.10 0.00
6_E 706_V 1.05 0.10 0.00
19_P 721_T 1.05 0.10 0.00
7_R 333_Y 1.01 0.09 0.00
7_R 410_P 1.01 0.09 0.00
4_P 361_N 1.00 0.09 0.00
18_Q 423_Q 0.99 0.09 0.00
19_P 446_A 0.99 0.09 0.00
19_P 534_A 0.99 0.09 0.00
17_R 642_S 0.97 0.09 0.00
6_E 87_L 0.97 0.09 0.00
5_E 663_P 0.96 0.08 0.00
15_E 496_A 0.96 0.08 0.00
17_R 168_Q 0.95 0.08 0.00
8_W 214_L 0.95 0.08 0.00
17_R 785_V 0.93 0.08 0.00
10_Y 686_L 0.93 0.08 0.00
5_E 232_T 0.93 0.08 0.00
19_P 442_F 0.92 0.08 0.00
7_R 99_V 0.92 0.08 0.00
1_P 520_A 0.91 0.07 0.00
19_P 459_P 0.91 0.07 0.00
11_I 702_T 0.90 0.07 0.00
5_E 615_N 0.90 0.07 0.00
18_Q 740_M 0.90 0.07 0.00
18_Q 711_A 0.90 0.07 0.00
15_E 363_W 0.89 0.07 0.00
12_K 91_I 0.89 0.07 0.00
7_R 401_V 0.89 0.07 0.00
15_E 279_S 0.89 0.07 0.00
15_E 438_I 0.88 0.07 0.00
11_I 586_L 0.88 0.07 0.00
9_R 256_L 0.87 0.07 0.00
10_Y 230_L 0.87 0.07 0.00
6_E 489_G 0.87 0.07 0.00
14_L 201_L 0.86 0.07 0.00
19_P 262_V 0.86 0.07 0.00
16_S 192_F 0.86 0.07 0.00
18_Q 367_K 0.85 0.07 0.00
8_W 579_N 0.85 0.07 0.00
1_P 83_Y 0.84 0.07 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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