May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
10vs14a_Staszek
Genes: A B A+B
Length: 86 125 194
Sequences: 241 3831 107
Seq/Len: 2.8 30.65 0.55
MirrorTree (Pazo et al. 2001) 0.15
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 0.01 0.06 0.00
2 0.02 0.07 0.00
5 0.02 0.07 0.01
10 0.02 0.08 0.01
20 0.02 0.08 0.03
100 0.02 0.14 0.15
∞ 0.02 0.19 0.51
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
27_T 62_V 1.51 0.60 0.00
54_A 17_V 1.40 0.51 0.00
84_E 45_I 1.25 0.40 0.00
65_R 107_E 1.19 0.35 0.00
65_R 112_L 1.16 0.33 0.00
54_A 18_N 1.13 0.31 0.00
56_A 70_A 1.11 0.29 0.00
12_E 40_G 1.00 0.23 0.00
65_R 42_Y 1.00 0.23 0.00
56_A 64_Y 0.96 0.21 0.00
26_T 42_Y 0.94 0.20 0.00
36_H 18_N 0.94 0.20 0.00
60_S 66_D 0.94 0.20 0.00
49_L 104_K 0.94 0.20 0.00
35_Q 87_L 0.90 0.18 0.00
46_H 26_L 0.89 0.17 0.00
68_L 34_E 0.88 0.17 0.00
55_I 46_R 0.87 0.17 0.00
8_H 89_V 0.87 0.17 0.00
23_H 117_Y 0.87 0.16 0.00
51_N 102_D 0.86 0.16 0.00
60_S 68_F 0.85 0.15 0.00
17_K 29_K 0.84 0.15 0.00
27_T 26_L 0.84 0.15 0.00
15_Q 46_R 0.81 0.14 0.00
85_E 55_E 0.81 0.14 0.00
75_P 67_I 0.81 0.14 0.00
3_D 40_G 0.81 0.14 0.00
31_W 62_V 0.79 0.13 0.00
80_A 101_M 0.79 0.13 0.00
50_L 48_I 0.77 0.13 0.00
35_Q 84_N 0.77 0.13 0.00
72_M 114_K 0.76 0.12 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)
ID Seq/Len Name Options I_Prob Status
3993 0.55 10vs14a_Staszek Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done
3907 1.05 10vs14a_-10 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3906 1.08 10vs14a_-06 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.09 Done
3905 1.11 10vs14a_-04 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done
3904 1.1 10vs14a_-02 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done
Page generated in 0.0286 seconds.