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OPENSEQ.org
SAC
Genes: A B A+B
Length: 432 274 706
Sequences: 3305 100 3
Seq/Len: 7.65 0.36 0
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 0.04 0.01 0.00
2 0.05 0.01 0.00
5 0.07 0.01 0.00
10 0.08 0.01 0.00
20 0.08 0.01 0.00
100 0.10 0.01 0.01
∞ 0.15 0.01 0.03
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 < 0.6).
ID Seq/Len Name Options I_Prob Status
4304 0 SAC Δgene:(1, 10) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
4303 0.04 SAC Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
4302 0.04 SAC Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
4301 0 SAC Δgene:(1, 20) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
4299 0 SAC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
4297 0 SAC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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