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OPENSEQ.org
Set1_1
Genes: A B A+B
Length: 446 354 747
Sequences: 554 1567 70
Seq/Len: 1.24 4.43 0.09
MirrorTree (Pazo et al. 2001) -0.01
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 0.03 0.00
2 0.05 0.04 0.00
5 0.05 0.04 0.00
10 0.05 0.04 0.01
20 0.07 0.04 0.01
100 0.08 0.05 0.04
∞ 0.12 0.06 0.09
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 (0.09 < 0.6).
ID Seq/Len Name Options I_Prob Status
6053 0.12 D1_GI1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done
6051 0 D1_GI1 Δgene:(1, ∞) A:(1E-02, 2) B:(1E-02, 2) msa: HHblits (2015_06) Killed
6049 0 D1_GI1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed
2527 0.1 D1_Gai1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
2470 0.09 Set1_1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed
2461 0 Set1_1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed
2459 0.03 Set1_1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed
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