May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
spoVAC-SpoVAEB
Genes: A B A+B
Length: 150 116 266
Sequences: 557 1031 1
Seq/Len: 3.71 8.89 0
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 0.01 0.00
2 0.00 0.72 0.00
5 0.00 0.74 0.00
10 0.00 0.75 0.00
20 0.00 0.75 0.00
100 0.01 0.76 0.00
∞ 0.07 0.77 0.00
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 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.75 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
10670 0 VAC-VAEb Δgene:(1, 2) A:(1E-04, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
10669 0 VAC-VAEb Δgene:(1, 2) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed
10668 0 VAC-VAEb Δgene:(1, 2) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed
8590 0 spoVAC (Bs) spoVAE(B) (Bs) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8042 0 AC-AEB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
8041 0 spoVAC-SpoVAEB Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.104 seconds.