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OPENSEQ.org
YfiR-N-same-genome
Genes: A B A+B
Length: 190 435 576
Sequences: 132 656 93
Seq/Len: 0.69 1.51 0.16
MirrorTree (Pazo et al. 2001) 0.78
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 0.13
2 0.00 0.00 0.13
5 0.00 0.00 0.13
10 0.00 0.00 0.13
20 0.00 0.00 0.13
100 0.00 0.00 0.14
∞ 0.00 0.10 0.15
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 (0.16 < 0.6).
ID Seq/Len Name Options I_Prob Status
1234 0.22 YfiR-N-same-genome-Jackhmmer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1233 0 YfiR-N-fusion Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1232 0.14 YfiR-N-synteny Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1231 0.14 YfiR-N-neighberhood-20 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1230 0.16 YfiR-N-same-genome Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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