May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cpdrclpx
Genes: A B A+B
Length: 118 103 207
Sequences: 90742 1830 490
Seq/Len: 769 17.77 2.37
MirrorTree (Pazo et al. 2001) 0.17
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 0.11 0.08 0.05
2 0.13 0.08 0.08
5 0.16 0.08 0.38
10 0.19 0.08 0.93
20 0.23 0.08 2.22
100 0.32 0.08 6.88
∞ 0.35 0.08 9.91
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
79_T 61_R 0.91 0.47 0.00
39_Q 89_A 0.85 0.41 0.00
62_V 87_V 0.84 0.39 0.00
47_L 89_A 0.83 0.38 0.00
82_A 99_L 0.81 0.36 0.00
39_Q 86_K 0.81 0.35 0.00
107_D 93_Y 0.78 0.32 0.00
76_M 55_V 0.77 0.32 0.00
49_L 83_Q 0.76 0.31 0.00
18_A 86_K 0.75 0.30 0.00
48_L 62_S 0.74 0.28 0.00
47_L 87_V 0.71 0.26 0.00
57_M 76_D 0.71 0.26 0.00
55_P 65_P 0.70 0.25 0.00
27_E 23_H 0.68 0.23 0.00
4_I 76_D 0.67 0.22 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)
Page generated in 0.0433 seconds.