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OPENSEQ.org
CskSrc
Genes: A B A+B
Length: 450 543 890
Sequences: 3539 2663 226
Seq/Len: 7.86 4.9 0.25
MirrorTree (Pazo et al. 2001) 0.14
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.07 0.00
2 0.08 0.08 0.01
5 0.11 0.12 0.01
10 0.12 0.13 0.02
20 0.13 0.13 0.03
100 0.15 0.16 0.10
∞ 0.19 0.20 0.23
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
301_A 347_V 1.05 0.16 0.00
90_E 412_V 1.00 0.14 0.00
436_L 360_L 0.96 0.13 0.00
278_L 462_L 0.93 0.12 0.00
368_D 303_A 0.89 0.11 0.00
333_F 415_F 0.85 0.10 0.00
158_S 512_E 0.84 0.10 0.00
310_F 376_M 0.83 0.10 0.00
204_G 456_W 0.82 0.09 0.00
373_G 414_D 0.81 0.09 0.00
201_I 147_V 0.81 0.09 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.235), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
ID Seq/Len Name Options I_Prob Status
2818 0.25 CskSrc Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2816 0.05 CskSrc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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