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OPENSEQ.org
secy-sece
Genes: A B A+B
Length: 443 127 567
Sequences: 1689 327 171
Seq/Len: 3.81 2.57 0.3
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.20
∞ 0.02 0.00 0.30
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 (0.3 < 0.6).
ID Seq/Len Name Options I_Prob Status
11182 0.44 SecY- SecE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
9227 0.01 SecYE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
0227 0.3 secy-sece Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed
0092 0.3 SecYSecE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) (2013_03) Killed - Shared
0091 0.28 SecYSecE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared
0090 0.01 SecYSecE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared
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