May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Fan
Genes: A B A+B
Length: 104 246 348
Sequences: 2268 3847 22
Seq/Len: 21.81 15.64 0.06
MirrorTree (Pazo et al. 2001) 0.51
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 0.11 0.07 0.02
2 0.12 0.08 0.03
5 0.13 0.10 0.04
10 0.13 0.10 0.06
20 0.14 0.11 0.06
100 0.15 0.12 0.14
∞ 0.18 0.17 0.36
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 (0.06 < 0.6).
ID Seq/Len Name Options I_Prob Status
9475 0.07 evolve2 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
9464 0.07 evolve2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
9463 0.05 evolve2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9412 0.42 Fan Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
9411 0.06 Fan Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
Page generated in 0.0212 seconds.