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OPENSEQ.org
P63092-p07550
Genes: A B A+B
Length: 413 394 730
Sequences: 2166 826 24
Seq/Len: 5.24 2.1 0.03
MirrorTree (Pazo et al. 2001) 0.33
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 0.07 0.06 0.00
2 0.09 0.06 0.01
5 0.11 0.07 0.01
10 0.13 0.07 0.01
20 0.15 0.08 0.03
100 0.20 0.10 0.09
∞ 0.23 0.15 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 (0.03 < 0.6).
ID Seq/Len Name Options I_Prob Status
2484 0.2 beta2_gas_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.00 Done
2465 0.18 beta2_gas_1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.00 Done
1318 0.01 P63092-p07550 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1317 0 P63092-p07550 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1316 0.03 P63092-p07550 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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