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OPENSEQ.org
3179-8
Genes: A B A+B
Length: 519 93 599
Sequences: 146 125 92
Seq/Len: 0.28 1.34 0.15
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.03 0.15
2 0.06 0.11 0.15
5 0.06 0.18 0.15
10 0.08 0.20 0.15
20 0.08 0.21 0.15
100 0.08 0.23 0.15
∞ 0.09 0.25 0.16
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 (0.15 < 0.6).
ID Seq/Len Name Options I_Prob Status
0306 0.15 3179-8 Δgene:(1, 5) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed
0305 0.11 3179-8 Δgene:(1, 5) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed
0304 0.16 3179-8 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed
0303 0.11 3179-8 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0302 0.11 3179-8 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed
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