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OPENSEQ.org
RadA-RecA2
Genes: A B A+B
Length: 458 348 739
Sequences: 1886 1825 37
Seq/Len: 4.12 5.24 0.05
MirrorTree (Pazo et al. 2001) 0.83
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 0.07 0.00
2 0.00 0.07 0.00
5 0.00 0.07 0.01
10 0.00 0.07 0.01
20 0.00 0.07 0.05
100 0.00 0.07 0.14
∞ 0.01 0.08 1.18
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 (0.05 < 0.6).
ID Seq/Len Name Options I_Prob Status
10335 0.05 RadA-RecA2 Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
10334 0.09 RadA-RecA2 Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10332 2.14 RadA-RecA2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10330 1.28 RadA-RecA2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.23 Done - Shared
10329 0.05 RadA-RecA2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
10325 0.15 RadA-RecA2 Δgene:(1, 100) A:(1E-06, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.02 Done - Shared
10324 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.32 Done - Shared
10321 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.10 Done - Shared
10310 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.34 Done - Shared
10309 1.29 RadA-RecA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
10303 2.14 infinite-E-80-Jack Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10302 1.28 infinite-E-80-HHblist Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.11 Done - Shared
10301 1.29 infinite-E-60-HHblist Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.06 Done - Shared
10300 2.14 infinite- E-60 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10298 0.2 RadA-RecA-interr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10297 0.05 RadA-RecA-interr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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