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OPENSEQ.org
K1-Ta
Genes: A B A+B
Length: 333 439 768
Sequences: 3620 740 82
Seq/Len: 10.87 1.69 0.11
MirrorTree (Pazo et al. 2001) 0.10
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 0.03 0.06 0.01
2 0.04 0.06 0.01
5 0.05 0.06 0.03
10 0.06 0.07 0.06
20 0.07 0.07 0.11
100 0.13 0.10 0.32
∞ 0.22 0.18 0.63
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 (0.11 < 0.6).
ID Seq/Len Name Options I_Prob Status
1290 0.27 K1-Ta Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1288 0.1 K1-Ta Δgene:(1, 20) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1286 0.1 K1-Ta Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1284 0.09 K1-Ta Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
1282 0.08 K1-Ta Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) Killed - Shared
1280 0.11 K1-Ta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
1276 0.1 K1-Ta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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