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OPENSEQ.org

yidC-Foc

Genes: A B A+B
Length: 210 79 284
Sequences: 2085 837 112
Seq/Len: 9.93 10.59 0.39
MirrorTree (Pazo et al. 2001) 0.67
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 0.01
5 0.00 0.00 0.03
10 0.00 0.00 0.20
20 0.00 0.00 0.39
100 0.01 0.00 0.71
0.06 0.02 2.54
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 (0.39 < 0.6).

ID Seq/Len Name Options I_Prob Status
0108 3.76 yidC-Foc Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) (2013_03) 0.00 Done - Shared
0106 2.65 yidC-Foc Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.12 Done - Shared
0104 0.39 yidC-Foc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared

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