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OPENSEQ.org
2g38
Genes: A B A+B
Length: 99 198 273
Sequences: 310 442 135
Seq/Len: 3.13 2.23 0.49
MirrorTree (Pazo et al. 2001) 0.44
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 0.07 0.17 0.26
2 0.10 0.20 0.27
5 0.13 0.21 0.34
10 0.14 0.24 0.40
20 0.18 0.28 0.45
100 0.23 0.36 0.64
∞ 0.24 0.43 0.66
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
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.49 < 0.6).
ID Seq/Len Name Options I_Prob Status
0177 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2014_03) 0.01 Done
0176 1.02 2g38 Δgene:(0, ∞) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.08 Done
0175 0.7 2g38 Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.03 Done
0174 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.06 Done - Shared
0173 0 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0172 0.49 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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