May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
myco7
Genes: A B A+B
Length: 187 303 452
Sequences: 1458 2264 743
Seq/Len: 7.8 7.47 1.64
MirrorTree (Pazo et al. 2001) 0.21
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 0.01
10 0.00 0.00 0.02
20 0.00 0.00 0.03
100 0.00 0.02 0.17
∞ 0.06 0.10 1.52
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
172_L 102_A 1.05 0.52 0.00
106_L 75_L 0.97 0.43 0.00
46_S 89_L 0.95 0.41 0.00
153_T 60_V 0.91 0.37 0.00
42_K 34_D 0.88 0.34 0.00
174_V 160_G 0.87 0.33 0.00
133_V 145_T 0.85 0.32 0.00
172_L 104_T 0.82 0.29 0.00
23_T 112_I 0.82 0.29 0.00
133_V 154_D 0.80 0.27 0.00
153_T 229_R 0.80 0.27 0.00
44_V 110_I 0.79 0.26 0.00
183_G 30_L 0.78 0.26 0.00
130_E 31_Q 0.78 0.25 0.00
43_N 234_L 0.77 0.25 0.00
77_G 234_L 0.77 0.25 0.00
65_V 177_D 0.77 0.25 0.00
182_L 242_T 0.76 0.24 0.00
174_V 80_S 0.76 0.24 0.00
133_V 52_Q 0.75 0.23 0.00
160_I 85_L 0.74 0.23 0.00
159_Q 177_D 0.74 0.22 0.00
153_T 162_S 0.73 0.22 0.00
58_V 230_I 0.73 0.22 0.00
42_K 33_A 0.73 0.22 0.00
13_L 33_A 0.72 0.21 0.00
93_L 72_L 0.72 0.21 0.00
104_F 188_H 0.72 0.21 0.00
113_V 75_L 0.72 0.21 0.00
8_K 112_I 0.71 0.20 0.00
17_G 165_L 0.71 0.20 0.00
104_F 84_G 0.71 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)
Page generated in 2.0098 seconds.