May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
sprB F
Genes: A B A+B
Length: 333 423 698
Sequences: 1031 64 37
Seq/Len: 3.1 0.15 0.05
MirrorTree (Pazo et al. 2001) 0.59
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 0.01 0.00 0.04
2 0.06 0.00 0.05
5 0.08 0.00 0.05
10 0.09 0.00 0.05
20 0.10 0.00 0.05
100 0.14 0.00 0.06
∞ 0.19 0.11 0.06
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
9425 0.13 sprB F Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9424 0.13 sprB F Δgene:(1, 10) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9423 0.09 sprB F Δgene:(1, 5) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9422 0.12 sprB F Δgene:(1, 5) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9421 0.12 sprB F Δgene:(1, 5) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9352 0.05 sprB F Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0329 seconds.