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OPENSEQ.org
jckhmmr
Genes: A B A+B
Length: 240 224 435
Sequences: 1723 1233 48
Seq/Len: 7.18 5.5 0.11
MirrorTree (Pazo et al. 2001) 0.89
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.05 0.01
2 0.05 0.05 0.01
5 0.05 0.05 0.06
10 0.05 0.05 0.08
20 0.05 0.05 0.10
100 0.06 0.12 0.31
∞ 0.10 0.16 0.73
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 (0.11 < 0.6).
ID Seq/Len Name Options I_Prob Status
9419 0.02 7-24sc-d Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9418 0.74 7-24sc-cjckhmmr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9417 0.2 7-24sc-c Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9415 0.02 7-24sc Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
8464 0.11 jckhmmr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed
8463 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed
8462 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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